Raiders of the Lost ArkTheme: The powers of GOD resulting in melting faces and spooky ass force ghosts.
Spoiler
Bonus: Pit of Snakes!
Temple of DoomTheme: Cultist Dark Magic resulting in pulling beating hearts from living folks and glowing red hot stones that only burn baddies.
Spoiler
Bonus: Alligator River Smorgasbord!
Last CrusadeTheme: More powers of GOD resulting in immoral knights, magically healing wounds, and rapidly aging punishment for choosing poorly.
Spoiler
Bonus: Catacombs of Rats!
Kingdom of the Crystal SkullTheme: Area 51/Ancient Astronaut extraterrestrial visitation conspiracy resulting in alien beings and UFOs (and more face melting.)
Bonus: Giant Killer Ants!
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This progression of themes is natural to me. If anything "The Last Crusade" does the most "going back to the well" of the series. The other 3 films keep the structure but introduce new and different supernatural themes that have seeped into our culture and become religions in their own time.
In Crystal Skull we leave the old superstitious Biblical relics behind in favor of a new, different kind of belief and theory. They even visually acknowledge this in the film.
Old beliefs are shed and cast aside in favor of newer, sophisticated ones. And so it goes.
Extraterrestrials and what they imply are all together as believable as the Biblical theories if not more so in some ways.
But both are firmly rooted in the category of mystery having no concrete proof without a healthy dose of 'belief' to support them. That leaves a lot of room for adventure and exploration ... and that's what Indiana Jones has
ALWAYS been about.