My problem with the movie is not that aliens are too unrealistic, it is that the whole alien-thing was absolutly unneccesary for the story.
As far as I can remember they pick up that skull somewhere, then go and want to return it to this temple-thing. The aliens come into the story, just in time to fire off some special effects and to effortlessly solve the plot. That is Deus Ex Machina on Kindergarden-Level.
No film that expects to be taken serious as a work of storytelling can solve its plot by saying "Aliens did it", "He was himself from the future" or "Well, guess that was destiny".
What if MacBeth had discovered that the witches were aliens, from the future? Would that have been a good story? Hell no, because we live in the modern age, were we are interesseted, or at least should be, in actual human minds, indstead of special effects, dragons and other nonexisting stuff.
So, let me get to that Holy-Grail-Argument, that has been hanging around in this thread.
Jep, the other movies had supernatural elements. They were fine.
And here is why:
The last crusade, for example, actually was about the search for the holy grail. From the frist ten minutes or so, everybody brags on about that thing. But meanwhile it was NOT necessary for the plot or the film being completed or good.
If Indiana had opened the last chamber, just finding a letter "Dear Indiana, I.o.u a grail. ~God." the movie wouldn't have lost any of it's charme.
Why?
Because it was about the father-son-relationship, about crazy nazi-stuff, about the quest, the sreach for the grail. That is the reason, why indiana couldn't take the thing to a museum. Because it was only a mean to drive the storyline, not it's conclusion.
Take away the aliens from the crystal skull and see what you get.
Nothing.
Bland Phrases, soft-sience nukes and Harrison Ford.