I thought Prometheus was horrible. Characters made no sense, scientists who behaved nothing like scientists, taking off their helmets just because the air is breathable, poking an alien creature just for giggles, and that's just from the top of my head. It's just not a coherent movie.
I can't defend Iron Man 3 because I haven't seen it, but if it's just Mandarin that's bothering people, that's just a decision that people didn't like, but the overall coherence could be there.
Prometheus was not fun to me at all.