At a presentation at E3 this evening, Masahiro Sakurai discussed why Super Smash Bros. is launching at different times on Nintendo 3DS and Wii U. In a nutshell, it comes down to debugging, Sakurai said.
Super Smash Bros. is a game of enormous scale, Sakurai said, explaining that there are several hundred people working on debugging the two titles alone. Releasing both versions at the same time would require thousands of debuggers.
Additionally, Super Smash Bros. on 3DS and Wii U both have a different architecture. Although they share characters, they are different games and require individual attention not just to complete but to debug as well.