Team Rocket's usually the one mentioned because they show up in two regions, and they were the first example shown. (from the games/anime anyways, I'm way out of the manga loop) In Giovanni's case, you fight him before the championship (the Elite Four + the existing champion, you have to beat them to finish the game basically) because he's the leader of the final gym in the title where he shows up. It's different with other games and depends on the story, mostly...