This is an ALTERNATE roster, I'm always up for improvement. I'd like to take suggestions so I can better it.
I'm going to give you my honest opinions on the characters you posted. I won't suggestions if you should replace them or not, just what I personally see.
Bowser Junior: Now Junior isn't my cup of tea, but he's still a very realistic decision. I still don't really think Mario will get another character, but you never know.
Paper Mario: I actually have a question for you here, are you counting Paper Mario as a Super Mario Brothers character as a his own Spin-Off franchise with his own character icon. Because if he does count as a Mario character I highly doubt we'll see two Mario characters, let alone one. I think you should pick either Paper Mario or Bowser Jr.
King K. Rool: No need to really mention anything here, K. Rool is perfectly fine.
Eirika: Eirika isn't really a likely Fire Emblem candidate. Especially over characters like Roy, Anna, and Lyn. Despite the fact that her game was one of the GBA games was part of the 3DS Ambassador thing, nobody is really interested in having her in over other characters.
Chrom: Chrom is the most probable next Fire Emblem character, I have nothing against you there.
Ninten: If anything Ninten is one of the less likely Earthbound characters. He is also the most unlikely character in your roster (In my opinion, anyways). Ninten doesn't offer anything new in terms of representing the MOTHER / Earthbound franchise other than the original one. Which, to be honest, nobody really cares about. If you're really hellbent on representing the original game, go for Giegue (Giygas's original form). But Masked Man and Porky are always good choices too. But a new Earthbound rep doesn't sit right with me and doesn't seem likely or needed at all.
Takamaru: thats good you picked him amen
Sheriff: Eh, I'm okay with seeing the Sheriff. But I think something to represent handhelds would be better (In terms of adding a historical character at least).
Skull Kid: Skull Kid doesn't hold anything to his name if we don't see Majora's Mask 3D, which won't be considered until after the next Zelda title will be released, that being Link to the Past 2 this holiday season.
Starfy: I think he sort of lost his chance in Brawl. There was some sort of suggestion in the game's code that makes it seem that Starfy was going to be playable at one point. Stapy's (Starly in the American game) trophy was located in the Fighter related section, where trophys from related franchises of the playable character would organized into. It's a common theory that Starfy is such a useless assist trophy because the second party company that does own him, Tose, was being resistant or difficult with making Starfy playable. So unless Tose becomes more open to seeing him in Smash, I doubt we'll see him too.
No Metroid Character: Now what bothers me the most is that you decide to not add another character for Metroid. You add one MOTHER, you add two for Fire Emblem, and even add Two new Mario characters. But why not Metroid? It doesn't have to be Ridley, but everybody really wants him. I mean you also have Dark Samus and Anthony Higgs. Both are perfectly viable choices outside of Ridley.
2nd Pokemon Trainer: Will not happen, adding another trainer takes away from what makes the Pokemon Trainer unique.
Newtwo: Okay I guess, I would much prefer to see Mewtwo being able to change forms at will but that is only a personal qualm I have with that.
Matthew: Matthew is okay, but Isaac is the main character in Golden Sun. Isaac is the more realistic choice if you're going with someone from Golden Sun, but they are generally the same in battle style (At least from what I can tell).
Little Mac: ye u gun get ur bike stoln
Mega Man: YOU GOT: added to a roster
Bomberman: I would like to see Bomberman. I mean he's crossovered with Wario before, so why not? But seeing as his a Konami character now, I'd say he's lost his shot at Brawl. May I quickly suggest a Namco character to add in his place?
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On your other characters possibilites, I only have to acknowledge two things.
Wreck-It Ralph: Ralph hasn't really done anything to deserve being in Smash Brothers other than being in the same movie as Bowser. If this was a Sega styled Smash Bros, I think he'd be a bit more realistic.
Cloud: Cloud has never appeared in a main stream Final Fantasy game on a Nintendo system. That practically kills his chances. If you're looking for a Square Enix rep, I'd go into Dragon Quest or look at the characters that appeared in Mario Hoops 3 on 3 and Mario Sports Mix. Those are the only Final Fantasy characters I'd ever think we could see.
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Overall with your fifty character roster, the main things holding you back are:
- Over Representation of Mario (If Paper Mario is a Mario character, he or Bowser Jr. should go)
- Over Representation of Fire Emblem (While the franchise is big four characters is just too much)
- Adding a new MOTHER / Earthbound Character (Especially if it's Ninten. I understand you believe in him, but as you can see he has practically no realistic support)
- Skull Kid (Someone who appears a lot would be a bit more feasible)
- No Metroid new character (Everybody wants one and now we've got three great character choices, two of which we didn't have for Brawl)
- New Pokemon Trainer (It won't happen, I'd keep Lucario or go for Zoroark / Genesect personally)
- Bomberman (As much as I love the guy, his restriction to being a Konami character kills it for him)
I'd give it a 7 out of 10