Sonic 2006 had a few things going on for it, to be fair. The Shadow's side of story was actually pretty fine, Mephiles was a cool villain who actually got things done, and the soundtrack was (as per rule for the Sonic series) full of great stuff. Unfortunately, Sonic '06 was too ambitious for its own good. It was a textbook case of what TV Tropes calls "Christmas Rushed" — as an anniversary celebration, it needed to come out at a certain date, and Sonic Team could barely handle it. In that regards, one can draw a parallel with Sonic X-treme, a similarly ambitious Sonic game which was Rushed, the difference being that X-treme ended up being canceled. So, if Sonic '06 was done right, what else? To start off, it was intended as a reboot of sorts for the Series, so it would be reasonable to assume some elements Sonic '06 introduced would carry onto the rest of the series. To me, that means realistic human renderings, as opposed to cartoon stylings of later games, less of a comedy emphasis which became prevalent after Colors, and the way characters are chosen to play (as in, you play as Sonic, but get to control other characters in certain areas). Plot-wise, it really depends on ending being as IOTL (with the entirety of events being retcinned out of existence) or not. The entire Sonic series would likely end up being completely different from OTL, as relaunching it with Colors would be unnecessary. For 20th anniversary, we'd probably get something Adventure-styled (again, one could argue that Sonic 2k6 was a spiritual successor to Adventure duology), butterflying away Sonic Generations and Sonic Mania.