Same roster for both versions, so the number of characters may be limited by the 3DS capabilities.
3DS makes some characters, like Ice Climbers, difficult to implement.
...so the 3DS and Wii U versions may not release at same time.
Don't expect many 3rd party characters. Mega Man may be all there is.
Gameplay balance will fall somewhere between Melee and Brawl.
Gamepad will not have any advantage over other controllers.
Official tiles are Super Smash Bros for Wii U and Super Smash Bros for 3DS
No tripping.
No plans for DLC.
You can customize your players somehow (but its not costumes, and its not anything you have to earn)
You can transfer your customizations between Wii U and 3DS versions.
Wii U and 3DS versions can NOT play against each other, and each has different levels.

Lot of details are coming in from various interviews with Sakurai