Also thought the philosophical/religious stuff everyone always raves about for making it an "intelligent anime" was just really basic, surface level. Like someone got in a Wikipedia rabbit hole and just started naming and fashioning stuff after what they read about so it would sound smart but didn't understand any of it well enough so they couldn't synthesize it into a good story that primarily utilized those elements.

You're not far off. It's a big mish mash of stuff that was in the pop culture of the time (like the dead sea scrolls) that Anno and Co thought sounded/looked cool with shit they liked from other anime.

Like, the reason the End of Evangelion has a mid-credits sequence is because Anno saw the theatrical release of the Ideon movies, which were played back-to-back with no intermission, and he liked that.

The only caveat is that the Gainax staff were mostly creepy otaku - there's an interview where Anno is weird and about one of the Ghibli film protagonists (Nausicaa, I think), and that's the stuff going into their work. Shoji Kawamori has made similar "by otaku for otaku" anime (Macross), but it isn't nearly as leering at teen girls as Evangelion.

I feel like it just produced more pretentious, horny teenage boys.

Yep, been one of those. Thankfully I grew out of it. I feel like Anno never did and that's the main problem with him lol