Well it's set in the 50's and is a homage to all those 50's B movies, plenty of which were about flying saucers and aliens so they do have reasons for taking that direction. No problems with the alien stuff myself, fits in perfectly with the ethos of the 50's. The themes of the movies are fine if you ask me, just badly executed in places.
I watched it again the other night, I still have the same problems, I actually really loved the first half of the film, probably more so than the first time I watched it, second half is a mess though.