As for axed characters...I'll list the clones and say which I feel could be cut:
Pichu - it's inevitable.
Falco - not really, I could see them capitalizing on new movesets for him.
Ganondorf - seriously, he'll have a new moveset so he won't go.
Dr. Mario - maybe as an unlockable Mario costume?
Young Link - only if the change his moveset, use masks or use weapons like megaton hammer, windwaker and etc
Roy - I like him better than Marth but he'd most likely get the cut.
Mostly agreed.
Pichu - Yep. He's a goner.
Falco - From where I'm standing, his odds aren't so good. He's probably dead and buried.
Ganondorf - Worst case scenario, he comes back as a boss-only character/Ganon. But he's definetly going to be in SE as a villian.
Dr. Mario - To paraphrase
Heart of Darkness: "Doctah Mario — he dead." I'm willing to bet he'll not be appearing as an alternate costume.
Young Link - Maybe Windwaker-ized, or masked. I'm hoping for the latter, I'll take the former. But his odds are looking more and more like a fool's dream.
Roy - Gone. (Caution: rant ahead.) And good riddance to the cheap, fire-sword-wielding schweinhund! (Rant ended.) Others may disagree, but he's gone for better or worse.
As for:
Ness - He's got his stage back. Yay. Pity he won't be around to brawl in it, except possibly with a very different moveset.
Marth - Actually, his odds are fairly decent. Ike has been touted as heavyweight brawler, noticably different from Marth. So will Marth return? It's not guranteed, but it's possible.