A name I've thought of before is Super Smash Bros. Skirmish. From my understanding, though, the Wii U version and the 3DS version won't be exactly the same - apparently the 3DS version is supposed to focus a little more on customization in some way - so I expect this will have some bearing on the title, and that it won't be exactly the same between the two versions. Perhaps they'll just add "U" and "3D" on the end of Super Smash Bros., who knows?
As for characters, it's a bit harder for me to focus on this since I've become less of a Nintendo fanboy recently (and more of a JRPG fanboy ^_^), but I've always wanted to see some more Metroid characters, since it's a pretty big Nintendo franchise but thus far only has one playable character in the Super Smash Bros. series. It makes sense considering how the Metroid stories are supposed to have a sense of isolation. Recently, though, they've introduced some good characters. Some of the bounty hunters might work, although they're rather minor characters - or perhaps we could have Dark Samus. A really big character that might work, though, is Adam Malkovich. He existed before, but it wasn't really until Other M that we got a better look at him, and saw him in combat, although to some degree he fights exactly like the other Galactic Federation soldiers. I think he has some kind of exclusive gun, though, that he uses later in the game.
With Kid Icarus being revived, some characters from there may very well be welcome, esepecially since Sakurai is working on that and will be working on Smash Bros.. They've shown the character Magnus in trailers, and he seems pretty cool, might be fun to play. There might be some other yet-to-be-revealed characters in Uprising they could include.
I'm interested to see what kind of third-party characters they add. They've said something about a Capcom character possibly appearing, and I think the best bet there might be Mega Man. I have to wonder how much they'll do with the third-party characters, though, if they'll add just one, or two, or even more, and if they'll keep the old ones or have them replaced.
I also wonder what the whole customization thing with the 3DS entails. A slightly more versatile custom stage editor might be welcome, but I'd much more like to see a custom character creator. This has a lot of potential, and may fit well under the kind of platform-exclusive feature they're likely to add to compel fans to buy both versions of the game.