I figure if anyone is reading the thread by this point, they don't care about spoilers.
Act One is about the Soviets going to amazing lengths in order to break into a US military base on US soil in order to steal the corpse of a Roswell alien, who is very magnetic.
Things that do not matter at all to the movie?
1. The alien corpse. Sure, they drag it out to the jungle of Peru for an autopsy, but they don't do anything with it. If they hadn't gotten it from the military base, the Soviets wouldn't have been any worse off.
2. The magnetism. Aside from cluing Indy to the location of the skull (because apparently these are special magnets; even Mutt knows that gold isn't magnetic), nothing else is affected by the magnetism.
If either of those things had been worked into the plot somehow, I would've been happier. But they weren't. Sloppy writing.
(Maybe bullets fired at Indy are deflected by the magnetism; or if the Roswell corpse had had some special defense against alien death rays or something. I dunno. They could've come up with something.)
Admittedly, the action sequence for the get-away was kinda cool. The nuke was ridiculous, but eh, I could accept it.
Act Two is about finding the crystal skull itself. All it consists of is running away from Commies (a good scene), going to a Peruvian asylum and finding a map on the floor (fair enough), and then exploring probably the lamest tomb out of the entire series. And some people come out of nowhere to attack, but they have no point. There's no trap, no puzzle, no real tension. Ooh, there's a scorpion, but . . . it doesn't do anything. It's a boring act.
Then the end of the act is, I suppose, getting away from the Commies. Ridiculous, but fun enough. Lots of groan-worthy moments. Tarzan? Monkeys? Crotch shots? Driving onto a tree? Ugh. And Marion looked like she did a few too many drugs, since she was completely unconcerned about the danger around her.
Act Three? Well, before we get to the aliens, let's consider the crazy Indians. Where did they come from? They show up, they are scary, and then they run away easily and are shot to death. Rather pointless.
The huge CG tower key that they open by draining it of sand? Interesting, sure, okay. But come on, give me the drama.
Oh, look, the Commies have them at gunpoint. How are they going to get out of this? Well, in Raiders, when everything was bleak, they were saved by knowing how to resist the power of the Ark. In Temple, Indy called upon the power of Kali. In Last Crusade, Indy let the old guy be foolish and choose poorly. Sure, in all of these situations, Indy doesn't save the day himself; magic saves him because Indy realizes not to meddle with powers beyond him, while the bad guys decide to meddle.
Here, though? Why the hell does Indy even want to return the crystal skull? He has no motivation. Apparently the skull telepathically told him to, but aside from mental domination, he has no reason to do so. He should've dumped the damn skull off a cliff and said, "Screw you, ruskies!"
And when he does take the skull back, the Commies just get torn to bits, while CG spins around them at high speed, and the people survive by . . . running away. Wow, that's heroic.
There are so many faults in this movie's story. It really needed some overarching thematic point. Instead it was like a bad D&D game by a GM who didn't have enough time to prep before the session. Fun from time to time, but forgettable.
Raiders was about not delving into powers that should be left alone. Last Crusade was about healing and the danger of obsession, as any good grail story should be. (Temple of Doom was sloppy, and I can't figure out its point.)
What could this one's theme have been? Well, it's during the cold war. It could have been about the danger of power without checks and balances. It could have been about how paranoia can destroy someone from within. It could even have been all gung ho patriotic about the power of free-will and capitalism over the unified front of communism. Instead, it seems to just be . . . fan fiction.
I think I've spent more time thinking about this movie now than the actual creators did. (Hooray for my own hubris.) I don't ever intend to see this movie again.