Leaving the politics out of it for the moment, the objectionalities in Crystal Skull were
* Unnecessary complication
Can anybody actually map the path of the crystal skull? I still don't know whether it was in Oxley's possession before or after it was in the government warehouse, if it ever was.
And why did the government build their most vital storehouse five miles maximum from an atomic bomb testing site? I would have thought that that would have pissed off the Ark of the Covenant and given everybody hemorrhoids (see 1 Samuel six; it really wasn't like Raiders at all).
And if the alien wanted to leave the planet but couldn't do it unless all the skulls were together, why hadn't it/they left when all the skulls were together last time, before one was stolen by the spaniards?
And if the aliens were in fact keen collectors of ancient artifacts, why didn't they put them in a part of the spaceship that wouldn't be destroyed by the stresses of takeoff?
And if there were only thirteen skeletons, what did the Roswell reference refer to anyway? Who were those copses?
The story was that whoever returned the skull got the power. They returned the skull, and nobody got the power.
Actually, my main disappointment was that we only got to see inside one other box from the warehouse, and that was one we already knew. What about Captain America's shield, or the Independence Day spaceship, or Cthulu? There was a marvellous site that listed possible crate nominees, but I've lost it.