I can explain the design ideas. Before I start I'll say I'm really proud of Bbrawl Sonic and am happy he's the one you picked to ask about (especially since no one wants to talk about Sonic), but I'll explain more before saying more about why.
I will say that we did sometimes reduce the magnitude of weaknesses, but it would be unfair to say that we sought to remove character specific weaknesses. Characters have in-built weaknesess and strengths that define their playstyle, and by seeking to maintain playstyles, Balanced Brawl didn't seek to change the dynamic of characters in this regard more than was necessary. In some cases, attacking a weakness head-on was necessary to avoid the "evil" of polarization. Polarization is the way some characters do much better against particular characters than others. In standard Brawl, Luigi isn't bad and can put up a great fight against most of the cast, but he's very polarized as he has very poor tools for dealing with the best disjointed characters. Stuff like King Dedede's chainthrow that only works on some characters is the most polarizing stuff by definition. Of course sometimes polarization is inevitable, but for a balanced game, we definitely did seek to minimize it as much as possible. Sonic's weakness in raw kill power when paired with his generally decent off-stage game isn't really polarizing. It's not good, but it doesn't particularly cripple him in some match-ups while not mattering very much in others. We can and did balance Sonic around this weakness.
Now onto Sonic and his changes:
http://balancedbrawl.net/characters/sonic/
Sonic is a plainly mid tier character in standard Brawl so he was entitled to a pretty decent upgrade but not a mountain of buffs or anything really revolutionary like the real low tiers saw. My analysis of how Sonic operates is that he's extremely mobile with decent attack speed and average damage output combined with a good recovery and off-stage game in general, but he's hampered by very bad range/priority and kill power. In terms of how he plays out in standard Brawl, he needs to across the board do a bit better and specifically could really stand a more notable improvement against "team disjointed" (Meta Knight, Marth, Mr. Game & Watch)... which is a pretty common theme for a whole lot of characters. Sonic doesn't have it quite as bad as someone like Luigi since he can use his mobility to circumvent their range which is a sound idea in principle. The problem is that when it's his only option it gets limiting, and his most mobile options also tend to be some of his less rewarding ones. Enter some buffs:
My first buff for Sonic that I think makes a very big deal was a 1% damage buff to dash attack. It seems small, but this is a move Sonic can get away with doing a whole lot that isn't very rewarding on hit. Making it do more damage allows this occasional annoyance move to actually add up quite a bit more substantially. If I'm sitting there as G&W dtilting like I don't care and you sneak in a dash attack, it matters that much more. In the long run, it weakens the value of me just zoning you with dtilts all day a bit.
You will also notice the changes to up smash. What these changes mean in practice is that, when Sonic hits with up smash, it's far more likely to hit with every hit. Remembering you can up smash out of running, it's pretty important for Sonic. In standard Brawl, I was always frustrated by how this move was kinda close to being reliable but wasn't really; it's really nice for Sonic to be able to count on usmash in Bbrawl since it's such an easy option for him to go to out of what he likes doing the most.
Sonic also of course can and often does grab out of a dash, and the changes to dthrow (his best throw at lower percentages) have two practical effects. One is that it's much harder to tech, which matters a great deal against better opponents, and the other is that even if they do tech it, it's still overall more rewarding for Sonic than before thanks to the positioning.
So Sonic likes running around a lot in all match-ups and is especially counting on that mobility to fight characters who have a major strength parallel to one of Sonic's two major weaknesses (range). Buffing what he can do while at his most mobile helps Sonic all around but is especially nice in those match-ups. You can also think of the down aerial changes in this vein. Down aerial is a move that keeps Sonic moving, and improvements to it just allow him to more viably keep moving around which is building up his biggest asset as a character.
The last thing that was really key for team disjointed is that Sonic in standard Brawl just plain lacks an option to poke at them when the situation calls for it. Being mobile is great, but having at least some option to compete with them on their turf is really important and infinitely better than no option. The closest he had was ftilt, and the move's speed and hitboxes make it pretty crummy at that purpose. Testing suggested to us that his really terrible down tilt actually had the perfect speed and hitbox alignment; the only real reason Sonic couldn't use it to claim at least a little ground in those poking situations was that it was so lousy on hit. It's now pretty awesome on hit (it hits them into a really nice position always and is now one of the "randomly tripping" down tilts like Zelda's, etc, with some pretty good odds) and, even better, very likely to shift the dynamic of the match toward the faster paced and chaotic gameplay that Sonic is stronger in. Down tilt has gone from a move you almost never use to a move that you don't use all that often in general but can really come through in the specific situation that call for it.
In terms of his problems killing, we decide to mostly leave that as a weakness but did decide that allowing him somewhat better options to close a stock could be attained without sacrificing his style. Sonic uses up aerial in tricky kinda high damage situations to score kills, and the crazy stunts he is usually pulling off right before he lands that uair just scream "Sonic". If one and only one kill move is to be buffed, it's this. His other big strength in this area, his off-stage game, was really due for some fun that was also pretty useful. Enter the Spring... which has all sorts of clever application that I'm sure you'll have no trouble finding.
The only change of major substance remaining on Sonic is the nair change. Sonic's nair in standard Brawl is pretty similar to Wolf's; both are spinning moves that come out pretty fast and keep hitboxes around forever but are all around very crummy and likely unsafe on hit if you hit with the late hitboxes. This kind of quick option is something that fits into their natural playstyles well for different reasons and is definitely something both really benefit from being good. Sonic's nair in BBrawl is now a legitimately good move which is hard to call a big deal for one concrete reason but helps him in a lot of small ways. Let's call it a final "general quality" change on Sonic.
The last change we note on that change list is the change to that bit, which prevents the obscure abuse wherein Sonic could be grab released out of his up special and not regain the ability to do specials. This is a general bug that is most important for Snake but also a factor for Pit, Lucario, G&W, and Sonic that we fixed in as many cases as we could (as it turns out, we weren't able to fix it on Lucario but were on all the others). It's a nice thing not to have to worry about, and fixing as many dumb abuses as possible definitely makes the game a better experience no matter which character you are using. Speaking of abuses, I'd point out that Sonic no longer has to worry about his poor jump break, which was most notable for allowing Yoshi to do an across the stage chaingrab on him.
Your concerns about the overall cast I think you can lay to rest. Sonic sees some benefits here as a few of the best characters like Meta Knight get overall worse, and in general, we followed a trend of buffing weaker characters more than stronger characters. Ike isn't especially better than Sonic in standard Brawl, but if he really were a 4 with Sonic being a 2, we wouldn't add one step to both. We'd add more to Sonic in that case. We are also looking at depolarized, compressed tiers so the need for change relative to others isn't as important. In standard Brawl, a mid tier like Sonic is on the cusp of viability, and we can argue whether he's over it or not one way or another (IMO not, but it's close). If in Balanced Brawl even the low tiers are clearly viable, being a mid tier suddenly sounds a lot better, doesn't it? If we just changed which characters are good, we wouldn't have accomplished much; this kind of effect was always the biggest goal. It's unclear where Sonic fell relative to the rest of the cast with the only real consensus being that he's not at the very top or the very bottom in Balanced Brawl (he's not played enough to get much data beyond that), but we know the region he's in is clearly viable and safe to use so it's good news for Sonic mains whatever the relative tier list actually is.
There's also a note on stages. If the Balanced Brawl recommended stage list is used, Sonic sees a small gain on the starter stage, no real change on the opponent's counterpick, and a decent gain on his own counterpick in most match-ups. In terms of starters, he's looking at the new stage that is pretty okay for him (WiFi Waiting Room) being a starter and his old favorite counterpick, PictoChat, being a starter. Overall a lot is going on with starters so it probably isn't that big of a win for Sonic, but I feel he does just a little better here than he used to. On the opponent's counterpick, some of the new or previously region specific options are kinda lousy for Sonic, but I don't think any are worse than Brinstar and Rainbow Cruise always were for Sonic so it's not like things got any worse. On his own counterpick, Sonic is looking at the possibility of Mario Circuit and Mushroomy Kingdom 1-1, both of which are fantastic for him especially as you remember that things like DDD chainthrow that abuse walk-offs are gone but that really nice bthrow Sonic has works just as well as it always did. Most people don't think of stages too much, and you can't really worry too much about them since everyone has positives when it comes to stage selection, but it's another nice balance factor that I think is another small + for Sonic.
This was lengthy, but I had been waiting to talk about Sonic for a while. I have real confidence in Sonic in Balanced Brawl; I feel he's very faithful to how he played in standard Brawl while being clearly a much better character choice for the purpose of winning. I hope you enjoy the game, including Sonic!
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Before, BBrawl was working fine. Now, when I load BBrawl, it just loads regular brawl, and freezes at the SSS. If i turn off my wii or try to activate the code from this "second VBrawl", my game freezes.
What should I do?
The freeze is caused by the lack of "no custom stages". If you try to play standard Brawl with the standard package Bbrawl SD card in your Wii, it freezes on the stage select screen. Obviously the .gct is not loading. The advice you've already received is mostly good advice that, if you follow, should probably fix your issues. If you have further issues, we can try to work through them.