In Iwata Asks about Kid Icarus Uprising,  producer Masahiro Sakurai revealed that the game was originally developed on the Wii and the PC since Project Sora didn’t have access to a Nintendo 3DS development kit at the begining of the game development cycle.

Sakurai stated: At first we didn’t have the Nintendo 3DS development kit, so we started making it on a PC. Oh, and for a while we were using a Wii to make it! (laughs)

source: iwata asks