I don't think there's any question that Sega could have had Prope make the game if they wanted them to.
Sega owns Sonic, so they can hire anyone they please to work on it, and unless Prope really didn't want to do it, I don't see why they would turn down a guaranteed hit.
In the end though, I don't know if it would have been much better off with them. Wasn't Yuji Naka behind Shadow the Hedgehog? And Prope hasn't shown anything too special off lately either, Let's Tap was a mini-game fest (albeit with some funky new controls) and their other stuff has been i-phone/handheld games.