What The Hell Happened:
You might think that the movie was the result of Steven Spielberg watching episodes of The X-Files and Even Stevens through an ether-soaked rag, but the real culprit seems to be George Lucas. The guy who invented Indiana Jones in the first place was also the guy ensuring that the fourth film would be a boulder-sized turd of suckage.
For starters, the reason there was such a long gap between The Last Crusade and Crystal Skull in the first place? Lucas insisted the movie had to be about aliens, which Harrison Ford and even noted alien groupie Spielberg objected to. At one point, they had a script by Frank "Shawshank Redemption" Darabont that everyone loved ... but Lucas vetoed it. (Darabont described him as "one of the most stubborn men I know.") Eventually, through Lucas' Force-like power of pure bullheadedness, he wore everybody down. Even though he didn't "believe in it," Spielberg agreed to include aliens out of friendship.
Neither was a friend of Cate Blanchett, though, or they wouldn't have given her that hairdo.
The one contentious moment that's become a focal point of fan rage over the years is the "nuke the fridge" scene, in which Indiana Jones survives an atomic blast by crawling inside of a refrigerator. The only worse lesson for children would be if Indy started playing with a loaded gun while bragging about how awesome crystal meth is.
Either way, meth was probably involved in this decision.