Resurrection and Prometheus were both great. For different reasons, of course. Though I'd probably say that my favorite aside from the first two is Covenant. Might have to think about that, though.
It's always a toss-up between the first and second, isn't it. I'd say Aliens is my favorite, but it's a hair's breadth of difference. My actual controversial opinion is that *all* of the Alien movies are good (except AVP 2).