I didn't have this problem so much, as I played the games before starting the anime. The only real anime-induced confusion I can recall revolved around gen 2, which I thought (before its release) would include the Orange Islands. As awesome as the Kanto-Johto combo was, I maintain that we need a game with the Isles included.
Oh, and Arbok evolves into Seviper. 'Nuff said. -_-