I'd say in hindsight SA2 was nowhere near the best Sonic game. But at the time think about all that was going on: The Dreamcast was at its height of greatness, Sonic was having his 10th birthday, there was a really fancy exclusive birthday pack, the SA2 demo disc in PSO v.2 built up a lot of hype, Shadow was a mysterious character, Eggman was playable, the plot was actually well executed and fun to follow. Tons of great nostalgic bits contribute to the love SA2 gets.
I remember at the time how crazy it was that Eggman would team with Sonic and that he had a grandfather. It was also very cool that Shadow gave his life to save the Earth and, at the time, was dead forever. He had this brief level of coolness to him until he became an emo zombie in future games. So point I'm getting at: Heroes and the Shadow game greatly hurt SA2.