I haven't seen Stargate since it first came out, but I do remember it starting with a speech given by James Spader that showed us actual archeological evidence to at least get our minds wondering if this was possible. In Indy, the only actual interesting archeological link is through the Nazca lines, but we are shown these in a book! Then faintly in the background of the cemetery scene, totally failing to ground anything that is to come. Not to mention that since we see aliens in the first ten minutes with no sense of wonder or magic or buildup, we just kindof dropped into a world where this stuff exists. Indy should build to the fantastic, not start the movie with it. There's a reason ROTLA, TOD, and LC start with artifacts that have no magical (or alien) properties.
Setup and payoff are the keys to a good movie (along with character of course) and Indy 4 has niether a good setup or a good payoff. "Talking head" exposition is not the way you build up anything.
Also, Indy and the audience see pretty much the same thing in the beginning of the movie (alien, nuke) as we do in the so called climax (alien, ufo).Look at the reveal of Akator... we cut form the gang looking at a skull in the rock, then Boom they're in a temple. The nice wide shot of the temple surrounded by jungle is wasted with a pointless chase down the steps then they go BACK up other steps to get into Akator. It's convaluted, and bland.
Also, regarding the genre, there is never a sense of tension or danger. Now this is due to several small things, but the biggest issue in my opinion is the number of people along for the ride. When you see Indy alone barely escape a situation, you can think that situation was pretty dangerous. But when you see 5 people (all but one being middle-aged, and one being insane) escape something, it obviously wasn't too dangerous to begin with.
Because of all of these things (and more) Indy 4 will never be a GREAT movie. But I think this edit (with your help) can make it a MUCH better one that at least doesn't piss off the fans. That's worth it right there.