Just tested it and its great so far,cant wait to see whos next in your roster.Bayou Billy perhaps (my Fave as a kid) or Fester from Festers Quest or Link? LOL
             
Bayou Billy (Has a decent chance of making it in, going to need another Konami representative
Fester (Will not get in)
Link (Is already Mario's helper)

Billy & Jimmy Lee is who I'm rooting for now. Especially after seeing Karate Champ.
Pretty good chance that they'll (well, one) will be in

Hey how about Rygar or Jason from Blaster Master. :3
Rygar (Maybe, there's another Tecmo representative that I have in mind so depending on that, Rygar may or may not get in)
Jason (I want to get someone from Sunsoft in but I'll have to figure out how he will play)

I bet you'll only use characters from sidescrollers, no?
It won't be just character from sidescrollers.
Some suggestions:

* Lololo Very unlikely, will probably be a helper
* Kid Dracula Unlikely...although I might have an idea for one of Simon's helpers now.
* Pimple Not sure, his brother Rash is more likely to be in however
* Nathan Spencer Very likely
* Bomberman Also very likely but needs his sprites to be redrawn
* Bill Rizer ...maybe. Given what he has, coming up with a move set will be hard and he might end up becoming a helper.
* Goemon Good chance of getting in, having a Japanese-exclusive character for Konami would be good
* Getsu Fuuma Will most likely be a helper at this point, Simon already has an alt. palette based off of him
* Firebrand Will most likely be a helper.
* Jackie Chan Not getting in.
* Kirby Is already Mario's helper
* Mega Man ...well, might as well blow the secret. He's the next one to be in.
* Ryu Hayabusa This was the Tecmo representative I had in mind originally, very likely to be in.
* Spy If you're referring to Spy vs Spy, won't get in.
* Strider Hiryu Oh man, how did I forget this guy? He might get in.
* Konami Man Forgot him too. Coming up with a move set for him should be interesting...
* The Noid Not getting in.

I made a few NES chars like Thomas and Mr.X from Kung Fu Master and Tetris, maybe can work for your game
Thomas is VERY likely to be in. I won't use your character but I could definitely use some elements from yours. Mr. X and Tetris on the other hand won't be in.

• Main Protagonist - If they were the protagonist of the first game of their series, they're eligible. Exceptions to this:
  
  • Donkey Kong Series - Mario is already in so someone else would need to take his place for the series. (either Donkey Kong, Donkey Kong Jr. or Stanley)
  • Bootleg Games - It's possible another Mario character could get in but only if their appearance is due to a bootleg game. (EX: Kart Fighter)
  • No Obvious Protagonist - At this point, it would just go by the most popular character or the one that could deliver the most unique play style.
• Originality - If they didn't derive from another media source, they're eligible. The only exceptions are those whose games were disconnected from their original source material elsewhere. (EX: Shatterhand and Kung Fu)
• Size - I'm trying to avoid having really small characters for this game. If the character's sprite is too small, they need to redrawn. However, some characters may not look right when resized which will end up keeping them away from being a playable character (but can still be a helper). Examples of this is Kirby and Lolo where if they were made to be big as Mario height-wise, they would be too large in terms of width and it just looks odd.
• Helpers - The way the helpers work is like this: One helper from the game and two others from the same games/series/publisher. Helpers that do come from another game have to follow the same rules above this. (not counting the size rule) If the character can't get 3 helpers easily, they can't get in.
• Moveset - This is were most of the characters will miss the chance of getting in, sadly. Here are the guidelines:
  
  • Obviously, I need to create a decent moveset for them that works in a fighting game and this is kind of hard. A majority of NES games are sidescrollers and some of them are quite projectile-heavy. Of course, I can always make new moves and play around with ideas if I have to but I can't stray too far away from how the character is or how their game was like. (EX: I can easily get away with this in Urban Champion despite what he can only do in his game. The fact he is a brawler leads to so many possible moves I could make up and not stray away from what he is) If I'm unable to give a character a decent move set, they can't get in.
  • I'm trying not to make any clones for this game so if the character doesn't have a unique play style I can come up with, they will not make it in. (EX: Hayate from Shadow of the Ninja won't make it in if Ryu Hayabasa is in since they would end up playing similarly.
  • I'm not including absurd/weird characters such as Tetris. It kind of falls under the first thing I said about being able to make a moveset for them. Even bad characters like Apollo from the Cheetahmen (if he does get in) will be taken seriously.
  • In terms of move sets, I'm only sticking with what's on the console. Nothing from future or past games will be used. Also, don't expect characters to play like they did if they appeared in a later fighting game. (Mario doesn't play like he did in SSB, Mega Man won't be like how he is in the Vs. Series and if they do make it in, Karnov won't be like how he is in Fighter's History and the Ikari Warriors won't be anything like their KOF selves. ) This is actually one of the reasons why Link didn't get in. He would be too similar to his SSB self if he used the tools he had available to him. References are fine though if they're not directly related to the character. (one of Simon's moves might seem a bit familiar to a certain Belmont's skill...)
  • I'm staying away from anyone that heavily relies on weapons to fight. Weapons used in specials and supers is fine but the use of them for every single move is not allowed. There are some exceptions (heck, Simon sounds like he shouldn't be in because of this) but if it's possible to make then punch and kick without it seeming so odd, it's fine. This was another reason why Link didn't get in. Without his sword, it wouldn't seem right to have him fight like that
• Representation - I'm trying to get characters from games we loved, we hated, were Japanese-exclusive, were American-exclusive and even bootleg games from all different publishers. (Nintendo will probably have the most representation, Capcom and Konami would only get about 3 or 4 characters, Hudson Soft would get 1 or 2, etc.) There's more emphasis on the "classics" with this roster so in terms of the other categories, it'll be kind of limited. (each publisher are allowed only one Japanese-exclusive character) This also means a popular character is more likely to be in. (hence, why Rygar may or may not get in) Characters who represent something specific about the NES/Famicom will also get in as well. (like a FDS represenative...no Disk-Kun probably won't be a character) Also I guess this won't be much of a surprise but females have a higher chance of getting in than males. (you can probably guess which games and characters I have in mind now)

Whoops! forgot to suggest Ryuhi from Hiryu No Ken, and i totally agree with Magma Dragoon, Rad Spencer has to make it in this game pleeease! 

my sugestions:
-some bootleg characters from bootleg games it can be awesome
-TMNT characters (but from arcade games not fighting game)
enough to say

OMG, always I wanted to see something like this in MUGEN, I'll totally wait for this fullgame

Spoiler, click to toggle visibilty

I made a few NES chars like Thomas and Mr.X from Kung Fu Master and Tetris, maybe can work for your game

So far, so good, but I'd suggest having villains as playable characters. Sometimes we remember a game because of its villain not its hero :p. Also: I recommend Ken/Kevin from street fighter 2010 and Black Mage from Final Fantasy!
And, from what i've played, zelda 2 link should be a regular character, and he wouldn't be like smash Link. Im pretty sure zelda 2 link uses magic instead of his regular items. He could be a slow and heavy hitter. His helper could be zelda? dark/shadow link? maybe ganon?

Some of the characters from Crash N The Boys/River City Ransom, Star man from NES's Pro Wrestling, batman from the NES games, one of the guys from Battletoads, or the characters from Yie Ar Kung Fu.

Why is it that you don't want to use the ninja turtles though? They even had a port of Tournament Fighters for NES which would make it fairly easy to convert any of them.

After messing with the build for a bit, somehow another mario appeared on screen. I think its from a helper, but it has happened to me twice so far.