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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.
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