Explain Ridley and Meta Ridley co-existing when they're the same character. (There is no way the space pirates would've been able to reconstruct him in that short amount of time.) Or Mario having FLUDD when it presumably malfunctioned after Sunshine's events. Also, Shiek is not related with Twilight Princess Zelda, at all, yet she's there as her transformation. Toon Link and Link are both in, and despite being different characters, were still of a different timeline according to the "canon" (lol), so that alone is a time paradox, same with Ness and Lucas. Also, Snake is presumably MGS1 Snake, yet he has Big Boss's face, who is a different character, and he is wearing his MGS2 suit. There's no canon here. Also, Diddy Kong's Brawl voice is VERY similar to his voice in Donkey Kong Country. Bowser and DK also constantly change voice actors. Bowser Jr.'s voice has no bearing on whether or not he can get in or not.
As for your Lyn argument (I can get behind Eiphraim needing Eirika). This is the game that has Wario in his Warioware appearance but the other members of the Warioware crew, who are of equal importance in the series, never appear. Captain Falcon isn't more important than Pico, Dr. Stewart or especially Samurai Goroh except for the fact he's the presumed main character. Lyn also appeared as an assist trophy, yet Eliwood and Hector are nowhere to be seen.
I personally found Zelda's moveset to be awfully bland anyway.
Anyhow, I got bored so I tried to make an ideal roster for the next game. Some choices aside (like, 4) I tried to make it as not biased as possible.
50 characters. All Brawl characters re-appear. 15 newcomers. (Around the same amount as Brawl's newcomers, but just like one or two more.) Blue border are characters that are unlocked from the start, whereas the red borders are "secret" unlockable characters. I also ordered them in what I feel like the best possible order. (Ex. the strategic games, Fire Emblem, Pikmin, and Advance Wars are in the same row. The NES-only characters are together. Punch Out, Metroid and Kid Icarus started as NES games that are popular particularly in the west so they're together. F-Zero and Star Fox together because of the space theme, etc.)
I couldn't decide between Captain Syrup and Kat & Ana, so I put both there for anyone to decide on whether a Warioware rep would be better than a Wario Land one. Kat & Ana could be considered filler for other Warioware characters not named Ashley.
Groose and Mewtwo are filler for their respective series. Groose less so, though.
King K.Rool, Lil Mac, Ridley, Chrom, Palutena and Samurai Goroh are the popularly requested character and the obvious choices, if you will. Mewtwo too if he was the Pokemon rep.
C. Syrup/Warioware rep serve as another Wario character, which is a big franchise to just have one representative.
Toon Link is iffy. I put Toon Zelda with him as another Ice Climber esque character because she fought with him in Wind Waker and particularly Spirit Tracks, and also to differentiate him from Link. Diddy + Dixie served as a huge hurdle for the development team, however, and I can see this being worse.
Takamura is the retro rep. But I also added another in Mr. Stevenson. He could be the "Mr. Game & Watch" character if you will, as he could represent the NES gun games. Of course, you could replace him with the Duck Hunt dog for that, but I'd rather Stevenson, personally.
Sami and Karate Joe are more personal choices, but Rhythm Heaven is huge in japan, and a character from the series is actually not that far from the realm. Japan would love him. Sami is kinda the opposite, because Advance Wars is pretty big in the west, and it's criminal not to have a rep. It's either her or Andy, but Sami's much more of a fighter. No one likes Max.
Ryuta (also Agent J) is another personal one, and he's DEFINITELY not gonna be in. So you could replace him with whoever you want. Karate Joe makes him obsolete anyway. Still, he'd be a great WTF choice.
Mega Man is who I can see as the most likely 3rd party rep. But you could look at him as a filler for that.
Thoughts? Like it? Not? Would you be happy if that ended up being the end roster?