Okay, I'm a little late to this party, but I'm reading The Complete Making of Indiana Jones, so it's simmering in my subconscious right now.
Everybody, including Lucas and Spielberg, and quick to point out how dark ToD is. What has always struck me about it, that nobody seem to mention, is how immature it is.
Willie is a screaming blonde girl, Short Round is a "Gee, whiz!" sidekick, the bad guys are so bad that they enslave kids... the whole thing feels like the kind of Indy film a ten-year-old would come up with, playing with action figures. Short Round is there as a kid viewpoint (Indy is a bit too adult a character for a kid to want to be, so if a kid is in an Indy movie, it's as a Robin sidekick). Willie is the kind of girl you think is the perfect woman when you're an eleven-year-old boy, and don't know what girls are actually like. The Temple of Doom is like an action figure playset, with real moving mine carts and a bridge that falls in half and drops your action figures off. Cool! Oh, man, bugs! Gross! Snakes! Those make girls scream! Monkey brains! Gross!
It lacks mystery. It lacks the sense of wonder for past lives and civilizations, now lost and crumbled to dust. In the other two movies, the search for the artifacts reveals something about the characters, a feature of the best adventure stories. In ToD, what does Indy learn about himself? I like kids, I guess?
In summary: Try to imagine John Williams's theme for the Ark, the one that plays in the Map Room at Tanis, as the soundtrack for any scene in ToD. You can't do it, can you?