Jesus, do we share the same brain or something? I'm starting to get freaked out here. Everything you said in your post is 100% what I think! I realize that Raiders is the best, but Doom and Crusade and Crystal Skull have become more interesting to watch, purely for their own unique qualities.
I also do not believe in God, and I am personally a big fan of good ol' pulp adventure (this helped me love Mummy 3, though everyone else wants to burn every last can of film on the planet...
). Therefore, I had an absolute blast watching KOTCS, cause I just go honky-dory over crazy stuff like Ancient Astronauts, UFO's, Lost Civilizations, Giant Man-Eating Ants, Hypnotic Bones, etc. I eat this up like chocolate, and I am proud to say that I am utterly, irrevocably, head-over-heels in gleeful fan-love with Crystal Skull.
I'd prefer science fiction to religious mysticism in an Indiana Jones flick any day of the week, so there ya have it. I have no problem with magic and supernatural in the old flicks (I mean, in the context of the story the religious aspect actually serves a narrative purpose and makes logical sense), but I am just naturally a sci-fi nutball from birth, I guess. I also love such stuff as Egyptian Mythology and Mesoamerican-themed adventure tales. This is why I dearly adore both Mummy and National Treasure series.
In short, dude, you and me are like the Inter-Dimensional Beings: of seperate body, but of a similar/single mindframe. My hat is off to you, my smart and logical friend.