A basic swap should be fine, however you might need to change power supply too and update software to take advantage of the onboard wi fi / bluetooth (for say connecting ps3 controller / keyboard etc)
I realised that I had only ever done basic update of retropie from version 2 to 3 which didn’t include a distribution update to Jessie. The pi3 builtin wifi/bluetooth firmware support i believe is only available in the newer distribution of raspian so I needed to do a new clean retropie install, which has been a bit of a pain remapping keys and setting up the right versions of emulators that work with my roms (i tried a distrubution update which took forever and in the end didn’t turn out too well - too many problems).
I’ve had a few network drop outs but I think might be due to not enough power as I haven’t change the power adapter yet. Other than that all ok, I can definitely see a performance improvement in for example some of the N64 games.