The fact most every 3D Sonic game afterward has been worse than it, thus making it the marker of "the beginning of the end".
Horrible voice acting from some of the characters (Tails, for example).
Awkward lines ("We kicked your ass BECAUSE WE'RE SONIC HEROES, lulz").
Horrible turning (nowhere NEAR as smooth as, most platform games).
Moves that require forward momentum, that will consequently be performed off cliffs.
Really asinine Special Stage requirements (get this key in the middle of the level before a really hard segment, then don't get hit at ALL for the whole remainder and you're in the clear!)
Forced to play more or less the exact same game four times to see the ending (I can respect the whole "Sonic is normal, Dark is Hard and Rose is Easy" aspect, but if you designed them as difficulty selections, then why are they all mandatory?)
Needlessly brought back Shadow, whose death was particularly heartfelt and meaningful, but now is completely pointless.
Brought the whole "bottomless-pit-fever" phenomenon to new heights - NOT a good thing.
Poorly thought-out team system (rotating team members is clumsier than it should be for a fast-paced action game), which relies on a large variety of actions being jammed onto the same button (which didn't work so well in Adventure 2, and is only getting worse with each new game).
I can probably think of more, but I'm too lazy by this point.
On the plus side, the music was excellent.