Interview with creator of Super Smash Bros.
On the differences between the Wii U and 3DS version, apparently the roster will be the same, but the levels will be different, accommodating the small or big screen respectively, and also having levels based on home consoles vs handheld consoles.
Which also means people on the 3DS will not be able to play against people on the Wii U. You can transfer your profile between the two, but players on the Wii U can only play against others on Wii U, and those on the 3DS can only play against other 3DS players.
So I'm a little conflicted. On the one hand, I'm pretty much settled on getting a Wii U someday in the far off future, so I'll have both consoles, and I'd like to sit and play on the TV with my wife and cousins. On the other hand, we can do that on our 3DSs (if my cousins ever get upgraded to XL) and I prefer the more traditional control scheme you get on a 3DS as opposed to the weird Gamepad and Wiimote stuff.