While we're at it with 3rd party characters, the thing that would make me happy for the rest of my life in terms of games, would be for Nintendo to get permission from Rare to stick Banjo and Kazooie in there.
That would be nice, but I highly doubt that we happen, since Microsoft owns Rare. There is already a ban on any Rare games that don't star Donkey kong on the Wii's Virtual Consle, so this makes the chances of Banjo and Kazooie's appearence in the game little-none.
Anyway, here are some other characters I would like if they appeared in the game:
Diddy Kong- Come on, he desearves it the most (well, along with Wario at least). Now that he's 100% owned by Nintendo, there is no excuse not to have him in the game.
Dixie Kong- If they have her in the game aswell, I'd rather have her as a seperate character than teamed up with Diddy, mainly because I wasn't exactly a huge fan of the Ice Climbers.
Sonic the Hedgehog- They might as well have him in the game, since he's more suiting for than Solid Snake.
Punch-Out!! Characters- Have Little Mac in the game. Have Soda Popinski. Have Bald Bull. Heck, even Glass Joe, Gabby Jay or Doc Louis (who isn't even a boxer). It doesn't matter what character you have in the game, just put any of them in.
Son Goku- Okay, so this is extremely unlikely, but Nintendo did publish Jump Superstars in Japan.
MissingNo.- Face it, Nintendo: MissingNo. is a Pokemon and you know it. Again, this would be highly unlikely, but come on, who wouldn't want to play as MissingNo.?
Wind Waker Link- I know WW wasn't exactly a huge fan favorite among Zelda fans, but despite what I've said before I started to have my own opinion, I did like it. I think WW Link would make a good substitute for Young Link for several reasons.
Also, here are some new stages I'd like to have:
PokeFloats 2- This time, with more Pokemon and such, but hopefully, little to no Ruby and Sapphire Pokemon.
Glitch City/MissingNo.'s Lair- As the name says, it would be based off of Glitch City, but would actually be MissingNo.'s home. Sometimes, things would go wrong, such as characters transforming into other characters, and such, but it would not effect MissingNo.
World Video Boxing Association Arena- Like it says, the boxing arena from Punch-Out!!. It could have alot of crazy things happening, like random boxers coming in to constantly punch at you and your opponent, as well as the ***** stole my, er, I mean the song that plays when Little Mac is jogging while Doc Louis is riding a bike while passing the Statue of Liberty.
Kastle Krush- As Mr. Wiggles had suggested, the castle from DKC2 in which the floor keeps going up. To make it even more challenging, you have to dodge all of the Kremlings that come through. Basically, it would be like the Ice Cliber level in Melee, but better.
Greenhill Zone- Obviously, the first stage from the first Sonic the Hedgehog game. The main obsticle in this stage is trying to dodge Dr. Eggman's attacks, which range from missle to a wrecking ball.
I'll think of more later.