The only thing that will probably always bother me is the soft-focus lighting in some scenes, like in the diner or at the end (avoiding spoilers here). It can't be because they were trying to make Ford look better...he looked fine in the more sharp, high-contrast shots. In the diner it looks like one of those late-nite tv ads for psychics, or a jewelery commercial; softened and airbrushed into obscurity.
After my first viewing of KotCS I watched part of Last Crusade again. Interestingly, I found myself viewing LC with the same mindset I had viewed Indy 4; sizing it up, being critical, almost daring it to be "good enough" for the series. And not surprisingly I didn't enjoy it like I used to. I watched some more of it today though, and loved it again.
That convinced me that KotCS is probably only mildly more flawed than the other movies, but still 100% Indiana Jones and a solid, if not sublime, addition to the series.