Kay, some of the characters I'd like to see, but probably won't:
Geno (Super Mario RPG: Legend of the Seven Stars)
Why he should be in: This is the most badass doll of all time. I mean, come on! Shooting stars out of his elbows?!? Also a fan favorite.
Why he probably won't be: he's a Square Enix brainchild, which already is grim-looking. If all Nintendo could get out of that game was one VGM for Fortune Street...
Samurai Goroh (F-Zero)
Why he should be in: Goroh has a pretty big role in F-Zero as one of the main 4. I feel like the game could use a more acrobatic and...off-kilter swordfighter.
Why he probably won't be: I don't know if there's a way to give him someone, without too much character depth, enough of a "kit" to make him worthwhile to play.
Slippy (Star Fox)
Why he should be in: he's about as iconic if not more so than Falco. There's a bunch of things that he could do, as a mechanic, that'd make him cool.
Why he probably won't be: while he'd be cool, he'd surely get annoying to play as and against after a while. If only he wasn't condemned to have that voice.
Banjo (Diddy Kong Racing / Banjo-Kazooie)
Why he should be in: Banjo is one of the unsung heroes of the Nintendo 64. A jack-of-all-trades adventurer, there's a ton of ways to fit him in.
Why he probably won't be: Banjo, like Conker, was a victim of the Nintendo-Rare split. Since his series was only prevalent in Nintendo for about ~5 years, my hopes aren't up.
Shiida (FE: Shadow Dragons and the Blade of Light, FE: Awakening)
Why she should be in: a speedy lancefighter would bring something totally different to the table. Also a pretty well-established character in the series alongside her husband.
Why she probably won't be: Probably not well-known enough as she isn't the star of any game. Also Shiida herself is super dependent so it'd be weird for her to fight by herself.
I can't think of any legitimate others...