Personally I think you're complicating things by not following the instructions on the BBrawl site...but you can do either two things. Study the structure of your other Brawl apps and copy one of them and replace the files that need to be replaced with analogous ones from BBrawl 2, or just back up your SD card contents on your computer and go with the easy route...
Eh since I don't have anything better to do, I am pretty confident that I can come up with a tier list for this game.
AA
Wolf
Falco
Pikachu
Peach
Zelda+Sheik
A
Squirtle
Olimar
G&W
ROB
Marth
Snake
Fox
Metaknight
Mario
Diddy
Sheik
Luigi
Pokemon Trainer (overall)
B
Yoshi
Ness
Pit
Link
Samus
King Dedede
Jigglypuff
ZSS
Donkey Kong
Toon Link
Ike
Captain Falcon
Sonic
Wario
Charizard
Zelda
Ice Climbers
C
Kirby
Ganondorf
Ivysaur
Lucas
Lucario
Bowser
For the most part most of the characters in this game are good and you would need the best of top ranked players to start showing where characters unfavorable matchups make them too hard to use in tournament. Anyone in the A tier and above is fairly secure for tournament and is liable to win under a skilled player.
I think most people aren't going to be surprised when I say Wolf is the best overall since he's well rounded in damage per hit, KO potential, and survivability. Don't get me wrong though, alone he's not going to render most of the cast unviable since usually his matchups should be no more than 55/45 in his favor since intelligent powershielding can get him punished, and his juggles and edgeguard don't **** anyone really hard.
If someone else is going to be a matchup offender however, this is where I get to Falco. Falco's playstyle is more specialized, and his survivability and to a lesser extent his ability to KO is less secure. However more characters are going to have problems dealing with a laser and SideB camping Falco due to how hard it is to punish significantly. Wolf however is a character that should have the advantage vs Falco, as well as Fox, as they both have good ways of punishing Falco for committing to his strategy, while he can't kill them quite as easily. Marth vs Falco isn't much different either, and ROB should be eager to try this matchup again with his new throw game being a significant threat to Falco's survivability.
Pikachu is a character who benefits more from hard matchups becoming easier. He is immune to counterpicking for the most part, and one of his biggest problems is solved by giving him a new fairly easy KO setup. A well played Pikachu doesn't have any insurmountable obstables, although G&W will still be an annoying matchup for him.
Peach is in a similar situation to Pikachu, but at any rate she's a solid character with above average damage output, a good recovery, good approach, and good edgeguarding. She's fairly difficult to stop from dictating the match due to her solid zoning options and she can punish a mistake hard. Marth can still make her life somewhat miserable, although he has to tread much more carefully in this matchup.
Zelda and Sheik together have all the tools you could want in a character. Sheik is one of the most reliable damage dealers by far with some of the most ridiculous punish and vertical spacing options in the game, and an intimidating closeup game, and alone would be a pretty solid character for tournament. Zelda has some of the safest KO moves in the game and plays keep-away well, and with a slightly improved recovery, new approach and poke tools, the duo supports each other well and is a threat at all times.
Anyhow moving to the next tier, with characters who generally should be watched out for as well.
Olimar is pretty much the same and now beats Metaknight like he was kinda designed to, and his iffy matchup against Snake is clearly better for him now. He doesn't make it to the AA tier since Peach and Falco are there to stop him, although his matchup against Wolf is probably fine for him. Marth and Mario however are hard matchups in his own tier that he has to watch out for, especially the latter who is a significantly buffed character who already was pretty good in that matchup.
G&W is an overall good character with high damage output and good KO options and edgeguards. He's a little slower than the other characters in the AA tier, Marth is not in his favor, and Wolf now probably wins slightly. His ability to stay competent on the stage list is his main asset.
Only two things hold back ROB, and it's a bad shield and a bad ledge getup, which unfortunately is pretty significant. He has to maintain momentum in his matches, but now has the tools to feasibly contain it. And most of his bad matchups became more manageable, while now ROB is a great character at scoring a KO when it's time to. ROB is good at getting grabs, and now with one of the better grab games, he's a force to be reckoned with. G&W is still a very hard matchup for ROB however, as he gains momentum against ROB very well, and can make it hard for ROB to get momentum back.
Marth is still a great character, but he must be more careful about his F-air zoning, which does less damage and knockback, and as a result is not quite as safe and rewarding. The removal of RCO lag however is a pretty good thing for him against Metaknight. Although he has a lot of good matchups, he has to be careful on the new stage list which can give him some problems. Metaknight still should be a problem for Marth fundamentally and Sheik in this game is probably a hard matchup for Marth as well.
Snake's biggest assets are still brokenly fast tilts with huge range, and making them weaker automatically gives Snake some problems as now he must compete with a cast who can kill him at respectable percents and juggle him more efficiently than the other way around, so some matchups like Sheik, Marth, Mario, Ness, Link, and Samus are all much harder for him. That isn't to say his tilts aren't broken anymore, and his explosives still have to be respected by all characters as option limiters, which alone leaves him no unwinnable matchups. Making Snake's Jab combo a reliable spotdodge punisher is great news for Snake. Consistently punishing a spotdodge for 14 damage is great especially against someone like Falco.
Fox doesn't live very long and doesn't have very good pokes, but he can camp well and punish a mistake hard. His new Jab combo isn't impressive, but it's a nice safe option to consider for option limiting against dodges. ROB and Luigi however are harder matchups for him now, and I believe Ganondorf is also quite competent against Fox, if not necessarily advantaged.
Metaknight as I understand him is now disadvantaged to Wolf, Falco, Olimar, and Snake, all matchups that everyone needs to be competent in. He's still definitely a great character, but pulling a win if he loses the lead can become tough if he has to wait til 160-170 or beyond to reliably KO against the majority of the cast.
Mario is slightly disadvantaged against G&W, Marth, and Metaknight, and ROB is likely to be a difficult matchup for him as well. He's overall however a good character with some great KO moves and spacers, and some technical but solid closeup options, but if he needs to maintain a lead, getting it in the first place can be difficult due to his low damage per hit. Of course scoring the first KO with relative ease can sometimes relieve that problem. Fundamentally it still can be hard to do when Mario has relatively weak forward options and when his fireballs by design don't usually start true combos. He does pretty well against Wolf, Peach, and Pikachu though.
Diddy is more or less the same, and it's not necessarily to his benefit. Banana locks are less powerful and his KO power is still on the low end. All in all nobody should be surprised he's good, but his game isn't outstandingly powerful enough to pull him to the next tier, and should he lose control of his Bananas, there are a number of matchups where it is more costly for him.
Luigi is a great character at first glance seemingly taking after Mario for the better, but that's not the entire story. Improved Dash attack is a great move for reacting to a dodge and for edgetrapping anything that isn't a ledge attack. Fireball buff is not just effective, but opens up a lot of room for creativity, giving him new edgeguard, combo, and approach options. He really still only has trouble actually legitimately setting up a kill in some matchups, and he rarely gimps or offstage KOs, so his game sometimes lacks the exact offensive tool he wants for the situation at hand.
The Pokemon Trainer in general is a good character, but suffers from bad recoveries, good camping, and Charizard and Ivysaur having some matchups that fundamentally give them problems. Squirtle alone is great, probably beats Falco (gets in, KOs and gimps more easily). Charizard is useful, not really because he has good matchups (he outright loses to Ganon lol), but because of his weight and the potential to punish a mistake extremely hard with him. Ivysaur is okay but still pretty easy to gimp, and that can cost the PT if it gets out of hand.
The next tier honestly isn't that much different in terms of character viability, but is separated from the previous one in that the characters have fewer particularly good matchups against the characters above them.
Yoshi is the star of this tier, and with his surprise factor, he could probably pull out a win in tournament, since most of his matchups in general got better for the most part. A lot of people still don't punish Egg Roll consistently, and the ability for it to break through some pokes and projectiles for a good hit makes it quite useful. Buffed D-smash is AMAZING for Yoshi and is what really makes him a new threat, with the ability to now actually kill things reasonably. Extra shield damage on aerials is kinda gimmicky. His approach still isn't exactly good, but his buffs do help prevent his opponent from fundamentally shieldcamping him.
Ness's better shield poking is obviously a good thing now that basically people have to chase after him to avoid letting him have his way offensively, but he still has zoning issues so Marth and G&W still aren't exactly fun or easy for him. And Peach iirc is supposed to be pretty troublesome for him as well. He has a decent shot against Falco and Wolf though.
Pit is a pretty good character, but he's still a little slow and Metaknight and Marth obviously are going to make him remember that even though he has a more powerful F-tilt and Dash attack to try to play with when zoning. Mario and Luigi are also going to make him suffer a bit when they get in with better closeup games. He's good against Pikachu though as I recall.
Link is still limited up close and easily juggled and edgeguarded, and he also has the problem of having a mediocre throw game which makes his grab not very threatening and risky to do in various matchups. However his new found KO power means making a mistake can cost his opponent dearly, and what is especially good for Link is the relative safety he has on a number of his new and improved KO options. His recovery while still not particularly good I should say is significantly better now that landing on stage is safer as well as getting slightly more distance. Buffed arrows are versatile in everything Link does. All in all while I think a lot of the upper tier characters, particularly Sheik still can make it hard for him to get control, I could definitely see a skilled Link main like KirinBlaze winning a BBrawl tournament.
Samus in a lot of ways works like Link, with less less destructive force on midrange spacers, but more ways to stay elusive and more consistent control up close should the fight come to that location. Despite this, Samus's matchups aren't too different from Link's, and most of the same characters give them trouble, but I give the nod to Link as I perceive him to be better against Wolf and Pikachu, while Samus I believe would have a better chance against Peach and ROB.
King Dedede is a specialty character. If Smash has a grappler, he embodies that concept pretty closely with its advantages and disadvantages. He wants to get close and grab you. He doesn't have a real approach besides sliding shield, but at the very least his grabs do much damage and provided he can land them enough, he can score KOs this way. Falco and Fox are still nasty to this character fundamentally, as well as Olimar, although Olimar does need to worry a little more about getting edgeguarded if he gets grabbed in this matchup. Samus now is a real threat to DDD as well, able to outspace him easily and threaten him with a KO from charge shot when DDD is forced offstage. Besides that his matchups against most of the cast are probably fine for him, and overall he's a more viable character due to other characters losing abuses on him.
Jigglypuff I don't see as having very many really hard matchups. Maybe G&W, Snake, and Ike in this game? This character is pretty flexible and has great spacing, and contrary to her appearance, she's quite capable of punishing a mistake pretty hard. The potential to bring a game to timeout better than most of the cast deserves a nod as well.
To be fair I have very little experience with ZSS. I do think that however that if there is anything going for her, it is the lack of experience most players have playing against her. Improving some of her bad moves well...is a good thing. And she can give some characters a hard time when she gets momentum. At the moment I believe she could do well in a BBrawl tournament, but the ability to neutralize most of her options with shield (due to her limited poke and grab options) may eventually hold her back.
Donkey Kong is pretty average in BBrawl. I would probably go so far to say he's one of the most "balanced" characters in terms of strengths and weaknesses in a sense, as opposed to "well rounded". He has some good tools, including some powerful poke and spacing options and some big punishers that kill obscenely early. He's a momentum oriented character and that's pretty much going to be his draw to fame. He will however have some problems fundamentally when you go to how he's a pretty weak character at punishing forward effectively (like Mario), and then he is one of the most easily comboed and edgetrapped characters in the game. While he does have a lot going for him offensively, he's still an exploitable character fundamentally. Mario gives this character a good deal of trouble as well as Olimar.
Toon Link is okay but doesn't stand out too much anymore. He used to have above average KO power, and while his KO power still is quite good, his damage per hit is still well below average. Outside of a decent matchup with G&W on neutrals, I can't see this character standing out in any other matchups. Partly because it's difficult for him to actually set up his kills safely, and because his throws aren't a really huge threat either.
Ike can get by, but still for the most part will run into walls against conservative playstyles. He does now at least have a real vertical spacing game and ways to juggle and edgeguard with some semblance of reliability, although his weak throw game is still a letdown. Characters like Snake, Falco, and ROB are still uphill by design for Ike, although he can now have more to do against characters like G&W and Marth.
Captain Falcon is a difficult character to use, so I could be underrating him a little. On the other hand Falcon still gets a headache when it's time to kill someone, since he still needs to trick someone or edgeguard/juggle at fairly high damage to get the KOs he needs. The Falcon Kick cancel does a wonderful job of giving Falcon something to do to get out of juggles and to increase his mobility. This character does however have really high damage potential either through his powerful followups after U-throw, shenanigans with Falcon Kick and Up-B, and Jab followups. It will take a Falcon user who can make the necessary reads for kills to truly make this character shine.
Sonic does kinda low damage and doesn't kill you very early, nor is he really able to land his kill moves easily. This is compensated for by the fact he's hard to pin down and has a solid recovery, which helps him extend his life. Aside from the improved D-tilt to make him less useless, his Spring edgeguard is fairly matchup specific in terms of effectiveness, although his improved D-air is pretty legit. Characters who can set up fairly easy KOs on him are a problem for him. Mario for example would probably be harder for Sonic to deal with than Luigi.
Eh Wario, nerfing his F-smash is a pretty big deal for him, as the move besides not killing as early well doesn't shield push as much anymore, which means it's less safe. Honestly though I could just be overstating how much he got nerfed, since he really should overall be fine with his spacing game which is infamous for being good in timeouts. I do think however he is a little limited when it comes to edgeguards, and Falco still beats him very solidly, and probably moreso with no chaingrab to threaten him anymore. He does better against Marth, DDD, and Snake, but everyone else is now much more able to take him on, which might be why I am not impressed with him.
Zelda really shouldn't be played alone. She barely has enough to scrape by with with an F-tilt poke, Naryu's love movement, and a fast dash attack to make up for a slow grab, although she has an easier time against DDD, Mario, the Ice Climbers, maybe a few other random characters.
The Ice Climbers are probably better than I give them credit for at the moment, although I will still berate them for having a below average recovery and generally becoming very iffy when separated. Maybe an amazing Ice Climber main can however prove that they are more than just a gimmick reliant on chaingrabs, and then we will see that the power buffs provided to these two characters are in fact something to be afraid of.
In the next tier, the characters I mention I believe have several clearly stupid matchups that will get in the way of them otherwise being viable characters.
Kirby can't really do much against G&W and Marth. He can't really stop them from controlling him, especially when being juggled or edgeguarded. King DDD is probably also worse for this character, with his new extra damage off of throw being a big deal for Kirby, while also not being pleasant for Kirby to recover against.
Ganondorf is quite bad against Peach, Mario, Jigglypuff, and the Ice Climbers, who all have a way of being very hard for Ganon to hit with his most important moves, and for the most part these characters also can do well gimping him.
Lucas has some big trouble against G&W and Marth, kinda the same way like Kirby. Sheik also really really messes this character up, being able to get in on him easily and gimp him very effectively, leaving him very few chances to do much of anything.
Lucario loses pretty badly to DDD. Not getting chaingrabbed anymore is great but he still isn't coming back very easily once he's edgeguarded, and he can't really poke DDD with any real safety for the most part. Besides that there are honestly a lot of characters he's not very good against since he really just doesn't have very good pokes, and he has a bad grab. He just has some walls here and there and can punish you hard if he lives long enough for Aura to do its work.
Bowser is overall the worst character in this game. Honestly I can't say for sure if he has any favorable matchups. He definitely has some bad matchups wherever you look. Olimar is still nasty to him. Link takes him down quite easily in this game. Ganondorf and Kirby win against this character. In this game, being so easily juggled, and having a recovery and ledge getup as horrible as Bowser's is something unaffordable. Especially unafforable for a character whose strengths are mainly on the ground, Bowser is a character who really cannot afford to take as many hits as his character design requests.