For the 40 Character Challenge
It is my opinion that there will not be more than 4 actual characters for any single series, and that the game would be better if they instead represented as many different genres as possible. So, here is my list, without any clones.
Mario Series:
1.Mario
2.Peach
3.Bowser
4.Luigi (Revamped Move-Set)
DK Series:
5.Donkey Kong
6.Diddy Kong
Yoshi Series:
7.Yoshi
Made in Wario:
8.Wario
Zelda Series:
9.Link
10. 11.Zelda and Sheik
12.Ganondorf (Ravamped Move-Set)
Pokemon Series:
13.Pikachu
14. 15. 16.Pokemon Trainer
17.Jigglypuff
18.Mewtwo
Metroid Series:
19. 20.Samus and Zamus
Honestly, I think they put in Zamus just give give a "new" character to the series, as Samus didn't really need to have this addition.
Starfox Series:
21.Fox
22.Falco (Revamped move-set)
23.Krystal
Kirby Series:
24.Kirby
25.Metaknight
26.King Dedede
Fire Emblem Series:
27.Ike
28.Marth
Earthbound:
29.Ness/Lucas (I am not sure which, but only one)
F-Zero:
30.Captain Falcon
Animal Crossing:
31.Animal Crosser
I think that an AC character would be doable, the "costumes" are random hats and shirts, and the player decides the gender. Also, you can choose a favorite outfit for your profile. Move-Set would include axes and other items from the series.
Nintendo Wars:
32.Andy
Dual-wielding wrenches FTW!
Pikmin:
33.Captain Olimar
Golden Sun:
34.Isaac
Kid Icarus:
35.Pit
Ice Climber:
36.Ice Climbers
G&W series:
37.Mr. Game & Watch
Third-Party Characters:
38.Snake
39.Mega Man
40.Sonic
40 characters, and a lot of different series represented, includes mostly core characters. Unfortunately, some really cool characters were cut from my list (like Ridley), but they would most definitely be added in if the list was 42 characters. I also thought about Starfy, as he would be an interesting Japan-only character, but from what I've heard, Sakurai doesn't want to emphasize Japan-only this time around. He would probably be character 41 though.