I think what ruined the film for me was that they showed you the aliens at the end. In the first film, the Ark kills all the Nazis but we never see God. Shiva doesn't rock up to burn Mola Ram's hand in the second. Jesus Christ doesn't walk out of the temple in the third. It was all left to our imagination. By simply showing us the aliens, it took away all the mysticism.
I can understand that but I also wonder whether the fact that the crystal skull was a body part of the "mystical" being means that to not show it whole would have denied the viewer an expected payoff or been anti-climactic. Might having not depicted the restored "alien" been on par with opening the Ark and having the Nazi's simply drop dead instead of the pretty-then-scary wraiths and face melting?
For the sake of conveying mysticism I suspect they could have done better than interdimensional beings but another religious artifact might have been too old hat. In my opinion, it was set up to be non-mystical from the start when they borrowed from Roswell and Area 51.
My thoughts on imagery-rich space battles: Revenge of the Sith's opener challenged me a bit too. I wanted to follow what was happening to this ship and that ship, wondered which ship belonged to which side, etc. It was spectacular, but perhaps too much so for me. And perhaps that is part of the point: "fog of war" for the viewer if I don't misuse the phrase. Some of the bigger battles in the various Star Trek series and Babylon 5 probably did this to me too, as well as the Alliance/Reaver fight in Serenity. "Pan back! I was still looking at that one ship!"
To be honest it's a similar effect for me during the Operations battle in Aliens.