Personally Sonic 2 is my least favorite of the Mega Drive/Genesis originals, even though I still think it's a masterpiece.
A lot of that has to do with the fact that it was the last of those that I played. I got my Genesis at the very end of its lifespan with the 6-Pak (includes Sonic 1) packed in, so when I wanted a new Sonic game it was Sonic 3 and Sonic & Knuckles that I found on the shelves. I rented Sonic 2, but didn't really spend time with it until Sonic Jam.
So, part of it is familiarity and nostalgia. At the same time, I didn't play Sonic CD until many years later, and although it has its flaws, I fell in love with it in a way that I never did with Sonic 2.
To me, it all comes down to Metropolis Zone. Once it gets to that point in the game, Sonic 2 just isn't any fun to me at all anymore. I understand peoples' dislike of Labyrinth Zone, but I never minded Labyrinth's exploration- and memorization-based difficulty one bit. It's the supernaturally annoying trap placement of Metropolis that frustrates me to no end, where an otherwise skilled player may know that a particular enemy or hazard is coming but still not be able to avoid it because of the irritating placement and trajectory.
Also, as mentioned above, while Sonic 2 has some great tracks, I don't think it's as consistent as Sonic 1 -- I think Sonic 2 easily has the worst soundtrack overall of the originals, honestly. "Hill Top Zone" and "Wing Fortress Zone" just don't fit in the series in my opinion. I think that they tried to theme the music too much with a middle-eastern vibe in Oil Ocean and a showtunes vibe in Casino Night Zone and it feels more gimmicky than cohesive. Like they're quoting music from our world instead of representing the alien, fantastical quality of Sonic's world.
I think that Sonic 2 also emphasized speed just a little too much. You have to play that game a ton before it stops feeling like a giant speed trap. I think people only started having that perception of Sonic 1 because they went back and tried to play it like Sonic 2.
I've always been surprised by the near-universal opinion that Sonic 2 is the best myself.
Metropolis Zone might have my favorite music in the series, though. It's close, anyway.