I'm of the mindset that Heroes was a good game, whose flaws were attributed to Sonic Team spreading themselves thin by trying to release it to too many platforms. It was their first Sonic game not on a SEGA console, and the finished product shows this. The History of Sonic book implies this as well, with Sonic Team pretty much admitting that it was a lot of work to get a game that played on PS2, XBOX and GameCube, and that the PS2 version suffered the most because of this. Really, I think it was the repitition that killed it for me. Once as Team Sonic was fun, twice as Chaotix was different (and I liked playing as them again), three times as Team Rose was too much, four times as Team Dark was too much. Also, they needed to tone down the character voices, way too much chatter.
Shadow was a spin-off, so I don't think it hurt the Sonic games for me as much as it may have for others. It has a lot of unique ideas that (according to the rumor) are being resurrected and refined. Really, the OutRun style progression was really a cool idea. But again, the game suffered from Sonic Team being overly ambitious and reusing the Heroes engine (correct me if I'm wrong, but I think it is a modified Heroes engine). Returning to Sonic Adventure 2 stages and plot elements was a cool idea, I did like the Prison Island stage.
'06 was shit, pure and simple. And thankfully it was this game that broke the camels back, and made Sonic Team realize they need to get their act together. Again, correct me if I'm wrong, but I thought a lot of those responsible for '06 did not continue on to future Sonic titles, at least in the high level positions they had before. Iizuka was not a part of it, Naka left during development and Shun Nakamura (director) has since only received a level design special thanks in Unleashed and went back to what he does best: making rhythm games like Rhythm Thief.
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Unleashed was a solid game. The art direction was very strong, music was excellent. There were far fewer characters, which lead to a more focused and simple story. The human character of Unleashed are really charming and lovable, really it's night and day when compared to '06's humans and adventure fields. The thing is, the werehog gameplay WAS polished and playable, and dare I say fun at times. Really, the problem was that the stages just dragged on too long. Werehog would have been a lot of fun if stages lasted 5-8 minutes. Instead, they typically went on for 20-30 minutes, which was really shitty. Also, the sun/moon medal collecting was not needed. The day stages were and still are praised as being the best aspects of the game, and since Unleashed, Sonic Team has refined this sort of Sonic gameplay which gave us Colors and Generations.
So I'd say we had four fantastic titles (Sonic 1-3&Knuckles), two good/great* 3D titles (SA1&2), one decent title (Heroes), one misguided not-too-bad-but-not-good title which is a spin-off anyway (Shadow), one shit title ('06), one game that got things back on track despite some flaws (Unleashed), and two great games (Colors, Generations).
Again, this is my opinion, so others surely differ. But still, I'd say the Sonic series has a lot more good than bad and has been solid in the main series department since 2010. Not to mention the Advance and Rush series have been enjoyable, and were very good Sonic titles during the years in which the console titles were not as good.
*nostalgia plays a factor in how good fans think the games are, as well as the ability to play and understand that these were achievements for their time, even if they haven't aged incredibly well for some
