I'm just about done watching TOD for the first time in a number of years (I'm going through the trilogy to prepare for the upcoming movie and related releases). I haven't gotten to Crusade yet, and I haven't seen that for a while so my opinion may change, but I always thought it was great and second only to Raiders. TOD is also great as an action film, but as an Indiana Jones film, it leaves some things to be desired. Specifically:
There's too much supernatural stuff going on. In Raiders, there's basically nothing supernatural until the very end, and as I recall Crusade was very similar. That's the payoff. I always thought of the world of Indiana Jones as being more or less grounded in reality (or as close as you can get with this kind of over-the-top action film). But in TOD, you have mind control, glowing magic rocks, people getting their hearts ripped out of their chests while they're still alive, and voodoo dolls (since well is voodoo Indian, by the way?).
Indy doesn't do any kind of investigating or discovering. The reason Indiana Jones is compelling compared to the average action hero is that he is an archeologist and uses knowledge to solve puzzles and locate artifacts. There's very little of that to be found.
It's still a great movie, but it is third on my list. (And I'll have to admit that I never realized that it was a prequel until today when I saw the date given at the beginning of the movie.)