Use Lakka instead of Retropie. 360 and PS3 controllers work great (plugged in—Bluetooth remains, as in most applications other than actual game consoles, a flaky PITA from what I've seen). I find the 360's dpad and face buttons unacceptable for retro games, but some people are OK with it. PS3 controller's pretty good. You shouldn't ever have a reason to mess with the mappings for either of those under Lakka unless you disagree with the defaults (unlikely, except maybe in MAME or something). Bonus for the PS3 controller is that the Playstation button works to kick you back to Lakka's menu, while IIRC the 360's system button doesn't (not accessible as an ordinary input), so it saves you having to use a button combo for that.
Lakka boots into Retroarch, which provides a unified I/O API to the "cores" (emulators) compiled against it. Even if you do manually map, you should only have to do it once.