I though the second R&C games was really nice. I liked the levels, characters and gameplay quite a lot. It's got one of those early R&C plots which had those 'evil mega corporations' themes, for most of the game you don't have the slightest idea what your actually doing, the weapons are really nice, and the minigames actually seem (to me) bearable and replayable.
I liked the second game quite a bit. Sure it might not be as good as R&C1 or R&C3, but to me it comes close behind those two. It certainly is a really good transition between the first and third game in terms of both story and gameplay!
EDIT: Oh and I do prefer R&C2 over R&C3, although I can accept that most people probably have it the other way around, and I can see why they would have it that way.