I believe Rayquaza and Kyogre will be in it for sure because Groudon is confirmed. Regirock, Regice, and Registeel will probably be in it, or atleast I won't be surprised by their apperance. Those three might replace the three legendary dogs from gold and silver considering some pokemon got axed from smash 64 to melee. They might even replace Lugia and Hoho with the legendary dragons from Diamond and Pearl. Wow, so many legendary Prokemon and there are alot more. I just think some of the older legendary pokemon will be replaced with newer ones.
As for normal pokemon, I can see some of the more popular 3rd and 4th generation pokemon in it. The origional starters will definitely make a return (or atleast in my opinion).
I would love to see Magikarp in it. He would do the same thing as Goldeen, but there will be a 1/4 chance that it will evolve into Gyaradose and use hyper beam for a 1 hit ko (or atleast a tone of damage with good knockback). I doubt it will happen, but it would be cool to see an evolving pokemon in the fray.
Moltras, Articuno, Zapidos-- The Three Legendary Birds
Regirock, Registeel, Regiice-- The Three Legendary Regi's (possibility of Regigigas)
Diamond and Pearl Dragons-- Replacing Lugia and Hoho
Mew and Celebi-- Still in there, but please actually do something!
Groudon and Kyogre-- Two Legendary Additions
Those should be the only legendary Poke'mon in the game, any more would be abusing it.
As for the other normal Poke'mon, I've mentioned the ones that really matter in previous posts. As for Magikarp evolving into Garydos, it's have to be a 1/10 probability, and it'd have to be more powerful than a legendary if it evolves.