Secret best Prime game. I agree that it has some pacing issues because of how the key hunts work in that game, but man that game has some killer ass atmosphere. The boss fights are dope as fuck too: Dark Samus, Emperor Ing, Boost Guardian.
The first two Prime games are masterpieces to me, and as much as I prefer the first one; I've never scoffed at the idea of someone arguing 2 being better. The stuff the game does really well, gives the game a richer texture that the first game couldn't match. One of those high points vs consistency thing. Both are wildly superior to Prime 3 though, that game was disappointing.