It doesn't top Sonic Adventure 1, as far as I'm concerned. To be frank, it did wrong a lot of the things the prequel did right, and add to the fact that both games have dated and partially buggy physics, I don't why it gets the praise that it does.
Let's start from the menu screen. You get to choose between hero and dark stories, which doesn't precisely change the gameplay, but it does change which perspective of the story you see. In SA1, however, you could choose individual character stories, which both determines the gameplay and the perspective of the story. The individual character stories definitely worked better, because rather than forcing to play speed stage, mech stage, emerald stage, rinse and repeat, the characters acted as individual game modes and had a level of consistency to them. I'd rather I could choose which character I play as per game mode, but SA1's story mode formula still works. SA2? I can't say the same.
Also considering the story mode, I really don't think SA2 did as good of a job on characters as SA1 did. In SA1, with the exception of Sonic and Big, every playable character had some sort of character development or change along the story, but SA2 forgets that development even happened and doesn't seem to show any story consistency with the first game. On top of that, the only two characters it seemed to have any real focus on was Robotnik (who is apparently perfectly fine with being called Eggman now) and Sonic's doppelganger.
I don't like how general gameplay was handled either. Eggman in a mech, fine, I liked Gamma's levels; but Tails doesn't need to be filling that gameplay too, he needs to be flying around, preferably racing people again. Rouge I couldn't give two shits about; as far as I'm concerned, the only reason she's in the game is to counter Knuckles' gameplay, and that's not much of a reason. The levels themselves are completely uninteresting, tend to last quite too long, and have largely a sense of linearity to them. In SA1, every single level was interesting; you were on a beach, in an amusement park, a casino, the outside of the Egg Fleet, the inside of the ship, so on and so forth, and the levels, while not quite mirroring the multilinear level design of the Genesis Sonic games, still had a sense of replay value in their design and were all unique in their own right.
Lastly but not least, the music in SA2 is not as good as that of SA1. As a matter of fact, I don't like how it stereotyped the levels at all. Sonic's stages are rock, Shadow's stages are rock with some... dark dude singing, Tails' techno, Eggman's techno, Knuckles' rap, Rouge's elevator music. In SA1, the music was made to fit the levels, not the characters, and what resulted from that were some very unique atmospheres for each level. The first part of Red Mountain and the mirror room of Twinkle Park are both brilliant examples of this. Even some of the character themes of SA1 I liked better than SA2. In SA1, Knuckles' theme had an almost perfect balance of jazz/funk and rap, whereas in SA2 it's basically all rap and the singer isn't even that interesting in the song. SA2's Sonic theme was okay, but I thought SA1 still had Sonic's edge; the melody, the roughness of the song, etc., whereas SA2's sounded a bit more... plain, I suppose you could say. None of the songs match the awesomeness of E-102y's theme, IMHO, so yeah.
A lot of people say that Sonic started going downhill in Sonic Heroes, but I'd say the peak of "modern" Sonic's career was SA1, for the reasons I just mentioned. Mind you, SA2 has redeeming features, but it still ignored a lot of the things that I think made SA1 such a good game, and so I don't think SA2 deserves anymore credit than its prequel.
EDIT: RANTRANTRANTRANTRANTRANTRANTRANT