Sakurai told Nintendo president Satoru Iwata that his Project Sora team made do with the other hardware available, including Wii:
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)
The combination of Nunchuk and Wii Remote seems like a natural match for 3DS's Circle Pad and touch screen. Sakurai also revealed that before the Project Sora team was fully together some staff members had created prototype videos of Uprising's air and land battles, which they used to share their vision with new staff.
You can catch the videos along with the rest of the Iwata Asks interview with Masahiro Sakurai, but be warned: may contain spoilers.