I could ramble on for days about this but I'm not going to.
All I'll say is that as a Smash Brothers fan and an artist I'm required by law to draw a picture of what I'd like to see in the upcoming sequel. And I did it now while my speculation is still relevant:

King Dedede: One of my favourite Nintendo characters, I'd consider it a failure if he didn't appear. But the chief director of the game also happens to be the man who designed Dedede, so there's a pretty solid chance.
Deoxys: I haven't played Pokémon for a long, long time but Deoxys was one who captured my attention and has become one of my favourite 'mon, and one of the few who would fit into the battle scene well. His transforming would make him a very tactical character.
Toad: They may have to fiddle Peach's attacks but I think Toad is the last Mario series character to deserve a place in the roster, so let's keep our fingers crossed.
Chibi Robo: I'm not overly enthusiatic about this, but I would imagine he would make an appearance in some capacity. ANd his game was great fun.

Pikmin: Would make a good item, I think. Different colours for different effects when thrown.

Levels: I'd like to see Bowser's Airship Fortress, Dedede's Boxing Ring and the Sanderson's House appear as levels, but as I covered those franchises with the characters, I went for a classic construction site Donkey Kong level.

Believe me, I could have written ten times this much, but I spared you from a fate worse than annoyance.