Harrison Ford having aged somewhat since Last Crusade made setting the film in the '30s implausible;
But more importantly, after the harrowing experience of making Schindler's List in 1994, Steven Spielberg felt he could no longer use Nazis as disposable mooks given the enormity of their actions in Real Life.
Saved from Development Hell: It took 19 years for the film to be released, mainly because it took that long for Lucas, Spielberg and Ford to find a script they liked.
What Could Have Been: Early script treatments (from the 90's) supposedly had Indy communicate frequently with the alien, who would have had a name and a backstory.
In one of the treatments, Indy has a daughter instead of a son, which lines up with the original version of The Young Indiana Jones Chronicles before they were edited to remove all the "present-day Old Indy" scenes. (Natalie Portman was rumored to play Indy's daughter before the final project and cast was announced.)