I skipped over a vast majority of this thread, so forgive me if any of this has been beaten into the ground and beyond.
I think it would be a fairly safe assumption that all of the characters that were in the original 64 version will return. They weren't cut in the trasition to Melee, so why would they be now? I would say the same of all the starters and "unique" characters in Melee. I don't see any of them getting the boot, but I suppose it's possible.
As for the clones, I would like to see some of them return with drastically altered movesets, and some taken out.
Falco: I like Falco as a character, but he really needs a moveset that differentiates him from Fox. The only major difference between them in the last one was the effects of their lasers. I'd hate to see him go, but if he's not going to be original then he's baggage.
Young Link: This guy can take a hike. Seriously. Does anyone ever main him over "regular" Link? He serves novelty value and that's it. If they really want to salvage him they should turn him into Link from Windwaker (even though I hated that game) and give him an entirely different tool set than adult Link.
Ganon: See Falco. Once again, I like him as a character, but he needs more to him than just being a slower, stronger Falcon.
Roy: Get rid of him. No, really. Don't even try to salvage him. Maybe he's huge in Japan, I don't know, but does anyone over here care or even know who he is? If they're really jonesing for another FE character to accompany Marth, there are a myriad of more interesting and varied characters they could choose from.
Pichu: What... You're kidding, right? Come on. Even if they changed Pichu so that his moves no longer pwn his own self, he would still be just another Pikachu. They've got, what, like 250+ Pokemon now? I know they can give us something better. The only reason to ever play Pichu is so that you can prove how much better you are than your opponent by humiliating him.
Zelda/Shiek: These two seriously need to be seperated into two entirely different characters. No one--and I mean no one--even plays Zelda as is. Really, it's not that she needs to get better so much as Shiek needs to get toned down... and Marth, and Fox, and... well, I digress. But my original point here still stands.