Here are my ideas..... NOTE: My list will be shortened at the end to the Top 50 characters
Mario Series- Mario, Luigi, Peach, Bowser, Petey Piranha, Bowser Jr., Paper Mario
Legend of Zelda- Link, Zelda and Sheik, Ganondorf, Tingle, Minda & Wolf Link, Skull Kid
Pokemon- Pikachu, Pokemon Trainer, Lucario, Meowth, Deoxys, Munchlax, Wobbuffet, MAGIKARP
Star Fox- Fox, Wolf, Krystal, Falco, Slippy, Peppy
Kirby- Kirby, Meta Knight, King Dedede
Metroid- Samus, Ridley, Dark Samus
Fire Emblem- Marth, Ike, Michiah, Black Knight, Roy
F-Zero- Captain Falcon, Samurai Goroh
Earthbound- Ness, Claus, Lucas, Poo, Paula, Jeff, Kumatora
Wario- Wario, Waluigi, Mona, Ashley, Kat&Ana, Jimmy T., Captain Maple Syrup
Donkey Kong Series- Donkey Kong, Diddy, Dixie, King K. Rool
Yoshi Series- Yoshi, Kamek, Baby Mario&Baby Luigi
Pikmin- Captain Olimar, Louie, Boss
Third Party- Solid Snake, Sonic, Megaman, Bomberman
Aminal Crossing- Villager, Resetti, K.K. Slider, Tom Nook
Retro- Ice Climbers, ROB, Mr. Game & Watch, Pit, Excitebike, Mach Rider, Balloon Fighter
Japan Only- Sukapon, Takamaru, Demille, Jill
Other- Isaac, Dr. Lobe, Dr. Kawashima, Andy (Advanced Wars), Mii
__________________________________________________________________________
Green - already in
Blue - more likely newcomer
Red - less likely newcomer
My Top 50 are as followed....
1. Mario - obvious
2. Luigi - obvious
3. Peach - obvious
4. Bowser - obvious
5. Petey Piranha - has potential for a very unique moveset, adds to amount of villains
6. Bowser Jr. - tough choice, adds to amount of villains
7. Link - obvious
8. Zelda/Shiek - obvious
9. Ganondorf - obvious
10. Tingle - I'm not very familar with this series, could be disputed
11. Minda & Wolf Link - apparently had pretty big fan base, another 2-in-1 character
12. Pikachu - obvious
13. Pokemon Trainer - I think they'll keep him with the same Pokemon
14. Meowth - tough choice, could be disputed
15. Lucario - has a 50/50 chance
16. Deoxys - could easily be wrong, could be form changable
17. Fox - obvious
18. Wolf - pretty sure they'll keep him
19. Krystal - adds to amount of females, different moveset than the other Star Fox people
20. Kirby - obvious
21. Meta Knight - very popular
22. King Dedede - very popular
23. Samus/ Zerio Suit Samus - obvious for Samus, 50/50 for ZSS
24. Ridley - VERY POPULAR, fans would freak if he wasn't playable, adds to villains
25. Marth - pretty obvious
26. Ike - pretty sure he'll return
27. Michiah - adds to female characters, not a sword-using person
28. Captain Falcon - obvious
29. Samurai Gorah - F-Zero NEEDS another playable character, also has a sword
30. Ness - pretty obvious
31. Lucas - pretty sure he'll return
32. Claus - adds to the amount of villains, could possibly glide
33. Wario - very sure he'll return
34. Waluigi - I know he hasn't appeared in any Wario games yet, but hopefully he will by then
35. Mona - could be disputed, adds to female characters, could have a unique moveset
36. Donkey Kong - obvious
37. Diddy Kong - pretty sure he'll return
38. King K. Rool - adds to the amount of villains, could have a unique moveset
39. Yoshi - pretty obvious
40. Captain Olimar - pretty sure he'll return
41. Solid Snake - pretty sure he'll return
42. Sonic - pretty sure he'll return
43. Resetti - could be disputed, probably will be one Animal Crossing rep
44. Pit - very popular
45. Mr. Game & Watch - pretty sure he'll return
46. Ice Climbers - pretty sure they'll return
47. ROB - he'll probably return
48. Sukapon - could be disputed, unique moveset, retro
49. Takamaru - apparently pretty popular, retro, swordsman, never really heard of him
50. Isaac - very popular, gives Golden Sun a rep
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Removed:
Falco - for Krystal, getting rid of a clone
Jigglypuff - I'm a huge Pokemon fan and even I want them to get rid of Jigglypuff
Toon Link - getting rid of a clone
EDIT: Added Kumatora and Captain Syrup for KumaOso under the large list, not Top 50.
Mario Series- Mario, Luigi, Peach, Bowser, Petey Piranha, Bowser Jr., Paper Mario
Legend of Zelda- Link, Zelda and Sheik, Ganondorf, Tingle, Minda & Wolf Link, Skull Kid
Pokemon- Pikachu, Pokemon Trainer, Lucario, Meowth, Deoxys, Munchlax, Wobbuffet, MAGIKARP

Star Fox- Fox, Wolf, Krystal, Falco, Slippy, Peppy
Kirby- Kirby, Meta Knight, King Dedede
Metroid- Samus, Ridley, Dark Samus
Fire Emblem- Marth, Ike, Michiah, Black Knight, Roy
F-Zero- Captain Falcon, Samurai Goroh
Earthbound- Ness, Claus, Lucas, Poo, Paula, Jeff, Kumatora
Wario- Wario, Waluigi, Mona, Ashley, Kat&Ana, Jimmy T., Captain Maple Syrup
Donkey Kong Series- Donkey Kong, Diddy, Dixie, King K. Rool
Yoshi Series- Yoshi, Kamek, Baby Mario&Baby Luigi
Pikmin- Captain Olimar, Louie, Boss
Third Party- Solid Snake, Sonic, Megaman, Bomberman
Aminal Crossing- Villager, Resetti, K.K. Slider, Tom Nook
Retro- Ice Climbers, ROB, Mr. Game & Watch, Pit, Excitebike, Mach Rider, Balloon Fighter
Japan Only- Sukapon, Takamaru, Demille, Jill
Other- Isaac, Dr. Lobe, Dr. Kawashima, Andy (Advanced Wars), Mii
__________________________________________________________________________
Green - already in
Blue - more likely newcomer
Red - less likely newcomer
My Top 50 are as followed....
1. Mario - obvious
2. Luigi - obvious
3. Peach - obvious
4. Bowser - obvious
5. Petey Piranha - has potential for a very unique moveset, adds to amount of villains
6. Bowser Jr. - tough choice, adds to amount of villains
7. Link - obvious
8. Zelda/Shiek - obvious
9. Ganondorf - obvious
10. Tingle - I'm not very familar with this series, could be disputed
11. Minda & Wolf Link - apparently had pretty big fan base, another 2-in-1 character
12. Pikachu - obvious
13. Pokemon Trainer - I think they'll keep him with the same Pokemon
14. Meowth - tough choice, could be disputed
15. Lucario - has a 50/50 chance
16. Deoxys - could easily be wrong, could be form changable
17. Fox - obvious
18. Wolf - pretty sure they'll keep him
19. Krystal - adds to amount of females, different moveset than the other Star Fox people
20. Kirby - obvious
21. Meta Knight - very popular
22. King Dedede - very popular
23. Samus/ Zerio Suit Samus - obvious for Samus, 50/50 for ZSS
24. Ridley - VERY POPULAR, fans would freak if he wasn't playable, adds to villains
25. Marth - pretty obvious
26. Ike - pretty sure he'll return
27. Michiah - adds to female characters, not a sword-using person
28. Captain Falcon - obvious
29. Samurai Gorah - F-Zero NEEDS another playable character, also has a sword
30. Ness - pretty obvious
31. Lucas - pretty sure he'll return
32. Claus - adds to the amount of villains, could possibly glide
33. Wario - very sure he'll return
34. Waluigi - I know he hasn't appeared in any Wario games yet, but hopefully he will by then
35. Mona - could be disputed, adds to female characters, could have a unique moveset
36. Donkey Kong - obvious
37. Diddy Kong - pretty sure he'll return
38. King K. Rool - adds to the amount of villains, could have a unique moveset
39. Yoshi - pretty obvious
40. Captain Olimar - pretty sure he'll return
41. Solid Snake - pretty sure he'll return
42. Sonic - pretty sure he'll return
43. Resetti - could be disputed, probably will be one Animal Crossing rep
44. Pit - very popular
45. Mr. Game & Watch - pretty sure he'll return
46. Ice Climbers - pretty sure they'll return
47. ROB - he'll probably return
48. Sukapon - could be disputed, unique moveset, retro
49. Takamaru - apparently pretty popular, retro, swordsman, never really heard of him
50. Isaac - very popular, gives Golden Sun a rep
__________________________________________________________________________
Removed:
Falco - for Krystal, getting rid of a clone
Jigglypuff - I'm a huge Pokemon fan and even I want them to get rid of Jigglypuff
Toon Link - getting rid of a clone
EDIT: Added Kumatora and Captain Syrup for KumaOso under the large list, not Top 50.