Sonic 2006 is a travesty of programming and design, there's really no comparison at all. 2006 is an objectively bad video game. There is no opinion involved.
Sonic Adventure is a great game that people always hated on for not being 2D sonic. It was even better than Sonic Adventure 2 in some ways. The way the various stories intertwined was fantastic.
The only legimate downside to Sonic Adventure was Big the Cat. I have no idea who thought introducing a fishing game to sonic the hedgehog was a good idea, but they must have promoted him later. Luckily, the game is designed in such a way that you can avoid playing any particular character's levels unless you are trying to unlock the 100% completion extra.