Well, as much as I hate '06, I personally included it as it did continue Shadow's story and in the end the time travel caused the whole thing to never occur. So no harm done to the overarching series plot. If anything, the time travel fix basically stuck Silver and Blaze back in the future so they have no hope of ever returning to the main series (here's hoping!). Also, '06 marked the end of the continuing storyline that Sonic Team was attempting to build since SA1. Still, I don't blame people for personally removing it. Hell, I wish Sonic Team themselves denounced it for the series.
Unleashed could be seen as a reboot, as it drops the whole United Federation/Shadow/Space Colony Ark stuff. However I think it's more of a house cleaning than reboot. All that stuff occurred before Unleashed, but Sonic Team chose not to mention it. This satisfies both camps, as Shadow could be chilling somewhere on the planet, it's just that we don't see him. Out of sight, out of mind, but not out of existence. Same for Empire City. It could be a part of the United Federation, and Station Square could be a few miles away, but they chose not to explicitly state these facts. Saves from needless exposition as found in Shadow and '06.
It has been hinted that the DS version of Colors will include additional story details not found in the Wii version, including cameos by Amy and Knuckles. And the Wii version features many badniks as seen in Sonic 1-4. So right there is proof that when Sonic Team wants to bring a character from the previous main series games back, they'll simply do so, bringing it back into sight and back into mind.