Well to my knowledge Sonic 06 was suppose to be a reboot, it was going to have all the characters but none of the backstory, which would have made sense as to why Shadow joined with G.U.N, the same people who gave him problems in SA2 and Shadow the Hedgehog, but with Generations proving 06 is canon with the rest of games, it caused even more issues. A real honest to god Reboot I think would work, if handled correctly.

I once, in my stupid moments, wrote a more edgy Sonic reboot. Where Eggman did take over the world and the rebel forces are pretty much just trying to back off as far as they can. In fact, Robotnik was once a great man who became paranoid and fought back because he was afraid he was going to be disposed of. 

Sonic, runs into Tails, a young fox who is trying to get into the Eggman’s city to find his missing parents. Sonic, doesn’t want to help at first, instead helping the fleeing rebel cause. But grows to care for Tails. Eventually, when Tails leaves for the city, Sonic follows, helping and eventually undermining Eggman’s whole expansion plan and toppling his control towers. Robotnik retreats, and Sonic realizes his true calling. 

The Chaos Emeralds in the game would be like Power ups you get that help when revisiting levels. Like one powerup would let you run on water, which would let you run across a lake in the first level and cut some time off your score. 

It would have featured a more open world and the levels are this big set piece moments. You’d be able to run up buildings when visiting Eggman’s city and yada yada. 

Oh well. Just ideas.