A lot of people seem to be having problems with the whole alien thing. My wife really didn't like that aspect either. She said that Aliens didn't fit because Indiana Jones is about artifacts with powers relating to God...which ever God that may be.
But I look at it like this:
What was Indiana Jones Really about? Indiana Jones was an archaeologist (is that how you spell it?). He's an archaeologist in this new movie.
Indiana Jones was collecting artifacts with these wonderfully crazy legends around them. In this new movie, he deals with Mayan and Incan stuff. Both of which have wonderfully crazy legends surrounding them. Some of which involve the theory that Aliens built their civilizations.
Indiana Jones always reflected the times he lived in. In the original movies, he was in the late 30's and he was dealing a lot with Hitler and his fascination with these godly artifacts. In this new movie, we're in the 50's....a time when the red scare was terrifying people...and a time when all of that U.F.O. stuff first started coming into play.
Indiana Jones dealt a lot with religious themes. In this new movie, the same applies. He deals with an ancient civilization's religion and their gods....they're just REALLY different Gods...It's like he says in the movie after he and Mutt see the pictograph of the god with the elongated head and Mutt says God doesn't look like that....Indy says, "That depends on what god you believe in".
So to me...it almost seems like a logical conclusion to go this route. Sure, there are other ways you could have gone..but I really didn't have a problem with this alien thing....or interdimensional being thing (a lot of people are starting to think these "aliens" that people have been seeing for years are actually beings from a different dimension....if you believe in that sort of nonsense).
My problem was with the pacing and overall story/character development of the thing. It just felt a little choppy to me. And of course the Lunacy of Lucas that was spread everywhere.