Im not sore about the aliens really, just the way that the MacGuffin was spoiled/given away in the 1st 20 mins.
It could have been awesome if was left to unfold at the rate that the other movies did.
Aliens, Arks, Shankara Stones, Grails etc etc are all potential paranormal things. Yet lets suppose they were all true:
They would have to be part of our natural universe, whether we currently understand their mechanics or the full mechanics of the universe at present or not. Not that the other movies were slavishly literal either, but we forgave the faux pas as the arose, due to how good the movies themselves were.
The rest of my complaints with the movie are like you say, physics and character/script based. Not that the other movies were slavishly literal either, but we forgave the faux pas as the arose, due to how good the movies themselves were.