I don't post here very often, but I do lurk around for info and...
The problem wasn't with aliens per se. A good Indy story with aliens could certainly be told. The problem was with the uneven, muddy, inelegant plot, juvenile storytelling, hamfisted dialogue and characterizations.
And the problem with the aliens conceit wasn't that they had power it was the manner in which biological creatures (with crystal skeletons ) had power and were turned into magical nonsense. How the whole situation got started was muddy and confusing at best. Why was one head missing? It popped off in the crash? Why did the skull of a now dead alien have psychic power? Why did all the skeletons merge together when 1 skull was replaced into one now living alien? Sure, a viewer can come up with an explanation to try and make sense of things but the movie offered nothing. Objects imbued with the power of god that'll zap you if you don't follow the rules/aren't pure of heart are straightforward, easy and clear cut and I can suspend disbelief for, not for goofy aliens.