You and I look at film completely differently. You see deep structural differences as inconsequential and superficial surface similarities as totally over-riding. But one of the buy-ins to the Indy series is that it's James Bond with an archaeologist. So he's going to go after religious artifacts the way Bond goes after world-threatening mcguffins. That's where Lucas and Spielberg started, but it's a non-starter for you. Did you really think Infodroid was going to change that?
The changes you like in TOD are why that movie didn't feel like Indy at all to me. Replacing the Nazis with Thugees (or whatever) was fine, but nobody makes better bad-guys than Nazis. But the real problem is at the deep structural level-- TOD has a man who was a skeptic about magic in ROTLA taking an earlier adventure where he uses magic like a superpower to save the day? The professor from ROTLA is nowhere to be found. Instead we have a womanizing, tuxedo wearing tough-guy who seriously says he "spares" people's lives. There are no Indy elements in TOD except the hat and the whip.
TLC is far from perfect, but at least the character resembles the guy from ROTLA. Instead of jettisoning the character, it expands upon him by doing the father story.
You seem to want the guy who discovers the actual ark of the covenant and sees it work to then forget about it and pursue non-religious artifacts? Is that a likely development? Would you? TLC is a natural follow up to the story of the Ark.
Crystal Skulls and Shankara stones, on the other hand, contradict the very clearly Old-Testament universe that ROTLA is set in.
