So lets see...it becomes so much clearer when the Ark blows it's lid skyward and everyone floats up into the sky, or the the Shikara Stones burn with "fortune and glory" and the Last Cup of Christ keeps you young as long as you stay within the seal. All these make so much more sense. I think alot of people miss the point. If this makes such a bad idea as a mythlogical MacGuffin, then what would you suggest in it's place???
They make more sense, if you buy into the possibility of a God putting magical properties into objects, because the artifacts are given a tangible history of how they came to be where Indy finds them as well as imbued with said power of God.
Major Eaton: What is this? Coming out of here.
Indiana: Lightening. Fire. Power of God or something.
Major Eaton: I'm beginning to understand Hitler's interest in this.
Brody: Oh, yes. The Bible speaks of the Ark leveling mountains and laying waste to entire regions. An army which carries the Ark before it is invincible.
Mola Ram: There were five stones in the beginning. Over the centuries they were dispersed by wars, sold off by thieves like you...
Indiana Jones: When they lost this rock their fields and animals died. They also said their children were taken from them.
[Mola Ram further establishes the stones mystical control of life by tearing out a still living heart thanks to the stones]
Grail Knight: But, beware: the Grail cannot pass beyond the Great Seal, for that is the boundry, and the price, of immortality.
[yes this is a weak caveat to the power of God, and merely a plot device to allow Indy to both drink from the cup and not live forever but also to save his father and bring about the destruction of the temple in the finale]
The stuff with the aliens was just too vague. Were they living were they dead? Were there many of them or just one? How did they come to be trapped skeletons with one missing a skull? The only thing firmly established is that "whoever returns the skull will gain great power" which turns out to be alien knowledge. The aliens, though living creatures like humans with physical bodies and mortality, which they establish via the cadaver, are much more based in science rather than religion. It's just left unexplained for the audience to accept as the skull having the power after death of magnetism, psychic communication, and reanimation of the skeleton body minus flesh and organs just because its alien.
I didn't expect a return to Raiders standards, my expectations were not so high they could never be satisfied, I just expected a story that was internally consistent and well written and didn't quite get one.