I don't see any noticeable decrease in intelligence from X to X-2. She wasn't a super genius in X. If anything, it could just be the fact she's less reserved and speaks more openly in this game.
Really, thinking on it, I can't recall any "massively stupid" thing she did in X-2.

Now Rikku...yeah, she totally did too much coke between games.

Paine was cool though. Makes me think of a hybrid Squall and Lulu. Her history with the Crimson Squad was also interesting.