I do think Indiana Jones and the Last Crusade is generally underrated. Not because of the script, which is a simple rehash of Raiders, but because the cast clearly had an absolutely great time making it and it shows in their performances.
Sean Connery steals every scene he's in, and even Denholm Elliott and John Rhys-Davies (Flanderized though their characters may be) are obviously having fun.
The tank chase could have done with a much leaner edit, though.
Conversely, I think that Indy fans tend to massively overrate Temple of Doom, which I find a poorly paced and quite frankly racist movie, with a completely unlikeable leading lady who was only hired because of Steven Spielberg's boner.
It also doesn't help that the numerous scenes deleted from that film explained a crucial chunk of the plot.