Wait, did somebody say Snake has no history with Nintendo? So that doesn't include more than one game on the actual consoles/handhelds? The NES games, the Gamecube games? Heck, if I remember right, there was some Gameboy(or Color or GBA) games, but that I only just remember. Either way, that's a load of bull. Honestly,
L
LunchmanJ
, you need to do a lot more research before making these statements.
First, Smash alone does not make a character relevant. Jigglypuff is a Pokemon rep in the long run. She did stay relevant in Pokemon in only specific cases(Gen VI gave her the Fairy type, which was the last time she was relevant since the Anime, and at best, her appearance in the spin-off Pokemon tactical rpg game, Nobunaga's Ambition). She may become relevant again in the latest Sun and Moon anime. Yes, part of her being in is due to being a vet, but it's only because she was originally added due to being a semi-clone to Kirby in 64(with some of the same Throws and A moves), which made her easier to add than Mewtwo, but that also worked because she was highly popular due to the Anime itself. A lot has changed since then. She's actually been lower priority in Brawl and Smash 4 because of not being extremely relevant at the time. Her ease of recreating the moveset is really all she has over Mewtwo now(who needs a lot more work because he's a lot more unique).
I don't need to explain Isaac to you again, but no, he is not currently relevant(and not all that recognizable. He's niche. He has a vocal minority for a fanbase. And while I do want him in, I doubt that'll happen while Golden Sun isn't getting any games. The series is on a hiatus at this time. After Dark Dawn did pretty badly, I can see why it's harder to throw the character in. And that's even assuming he would go for Isaac. There's more than one notable character. Alex is a stand-out among the games, and relevancy would've more likely gotten Matthew, who, while not as popular at this point or nearly as exposed to some, may cause more controversy. On the other hand, either could if a person likes the other more. But that's kind of how it goes with multiple protagonists of a series in general). For that matter, requests don't automatically get someone in. We've seen that even through the ballot. Requests are part of it, but they need to be realizable(this means moveset potential, relevancy, and fitting any other criteria at that particular moment that the developers see fit. Bayonetta was chosen because of these factors. We don't know exactly what criteria Sakurai was going for. It could be he wanted a 3rd party, and Bayo was the best choice there. But she fit the other two categories the best. A new gimmick(moveset potential), extremely relevant, and very easy to license. Last point to note is that she was in the top 5 in all regions, which is the most important part for a ballot. Taking everybody into account).
Due to how business works, Sakurai actually had to build his rosters heavily around relevancy. Not every single option, obviously(retros and 3rd parties are bigger exceptions at times), but this is how he can determine which ones will easily be recognizable. However, you're forgetting Smash 4's character theme; the gimmicks. Practically every new character had one except the clones(that is, the costumes turned into clones). That was the point. This changes a lot. We don't know if the next Smash will concentrate on that either. That was Smash 4's unique character selection point. Sakurai even said that himself; "Characters should have something they and only they can do." Now, he did say it before Smash 4 itself, but the point wasn't entirely a gimmick, but more uniqueness. The gimmick also happens to fit into this philosophy. I'm not saying a lot of characters should be looked over either. I'm saying that you're forgetting why his character selection was picky in the first place. Requests aren't enough. Moveset potential that makes a character feel unique actually matters more.
As for Brawl's so-called character hatred, it did have some unpopular picks(but only at first). Snake got only a little due to feeling like he was more of a Sony character. He did have Nintendo appearances prior to the series(but he wasn't even added outside of a request from Kojima due to what his son wanted. That's the only reason he got in). He fit the artstyle, and didn't exactly stand out beyond being what you'd expect from any 3rd party, which is "This isn't a Nintendo character". Sonic got heat too just because he was a 3rd party character, and being from Nintendo's original rival company(Sega) didn't help either. He was accepted easier because he felt more "kiddy" and "cartoony", of course. This applies to every 3rd party. R.O.B. got heat too, although it's really not clear why for many. Yeah, he was a toy at first. One issue is many didn't realize how important he was to Nintendo and Gaming's history. Many people weren't born around that time, or didn't do the research. He didn't reappear till Mario Kart DS, so he wasn't easily relevant to the fan's eyes. And technically lacked currently relevancy(but that's kind of how retro picks work. They aren't picked because of relevancy, but because of their unique history in gaming and what they can now contribute as a moveset. They all had something important or of note when chosen). I think those were the only super controversial ones. There was a bit towards Zero Suit Samus, but only because they took her original design and made her a far more sexy version with tight spandex and a larger chest than the games depicted normally, which didn't sit well with some, as it made her look sexualized(combined with her actual dialogue being closer to a dominatrix, which, while Samus was definitely a strong woman in how her characterization was designed and applied, although more with body language than dialogue at the time of her games, which made the sudden voice jarring and felt somewhat out of character to many). Some did get heat for "apparently"(which is only maybe true in one case of Toon Link replacing Young Link, and that's only really a viable theory, not even confirmed) replacing others too(Lucario for Mewtwo, Ike for Roy were the other ones. Neither were the case.)
Also, I want to correct you on your Capcom points. Capcom Japan owns MegaMan. Capcom USA owns Ryu. They are actually different companies, although obviously connected. Related, DLC isn't any more special than the others, but DLC also is viewed differently among the fans because they have to pay extra for characters. They can easily be more controversial if it someone they didn't want. Some already raised an eyebrow that "Capcom"(do note it's again, two different companies) got 2 characters. Some even forget Bayonetta is owned by Sega, and see her under Platinum Games(who did create her, and did make the original game, but Sega still owns the character).
Lastly, while I agree that Yoshi is a Yoshi rep now, Smash 4 already showed that he doesn't necessarily have to be as separated from the Mario franchise on the roster to make sense in Sakurai's eyes. He always did treat Yoshi, Wario, and oddly enough DK(despite originating at the same time as Mario, only showing they have the same universe/are connected) as Mario sub-series. Not counting how they're all near each other(bar the clone corner), he didn't want Yoshi separated from Mario's set of characters. I disagree with how he did it, but that's what he did. When he was put in the roster placement, it was still in order of major appearance, so he came after the rest of the regular Mario characters before the new generation of them(Bowser Jr. and Rosalina). If you're not aware, many did find this jarring since he was treated as a unique series from Smash 64 onwards.
Last thing I want to say, though; For the purpose of Smash Bros., a character series' rep depends entirely on their symbol. This is why Mii Fighters is treated as a Smash Bros. representation. Part of it is obviously because they're the new Fighting team, but the other is that their moveset is entirely created as a SSB thing. They don't represent the various Wii series at all, beyond the fact they're Miis. They weren't designed that way. Simply put, you should realize that nearly every character will still be a representation of the series their symbol shows. This can obviously vary in execution. Ness doesn't actually have a lot of his own moves, but he sure represents Earthbound's psi skills well due to his specials(which covers moves his team in Earthbound uses). Series will multiple reps(say, Mario) focus more on what that character does normally, instead of stuff concentrated on what happens in their games overall(as noted with the Earthbound point). Earthbound/Mother only had 2 reps, and Lucas followed the same design style as Ness, which is to use various Psi from his party members, less so from himself only. They are clearly meant to show off stuff from the games themselves, not so much what they normally can do. Mario's moves, on the other hand, are stuff he actually does. Ganondorf is a perfect example of it being unique in execution. While he did originate as a clone, that also did a lot of what he was capable of in return. He was actually a pretty brutal physical character with magic in OOT, his artwork even depicting him attempting to punch Link with an overhead strike(which is basically his Forward Air attack, something Falcon doesn't have. Likewise, Ganondorf's design in Smash is a represented of what the Triforce of Power can completely do, which is increase the power of the user. It's not just "turn into Ganon", which is only just one ability, and that's only due to storyline reasons that need a spoiler to understand. Ganondorf is a powerful magic user. Using magic to increase the power of your moves is actually a very reasonable ability that fits him pretty well. Obviously he was still a clone due to circumstance, even being the only reason he got in. what he was about, murderous power).
Long post, but make sure to look at every unique point. They all note some issues with your roster. And I won't be getting entirely into your other various choices, just explaining a lot about what Smash is designed like, so you understand some points of the official roster selections more.