Count me in the ranks of the underwhelmed. Although like a lot of movies I might like it better the second time around. Here are the problems I had with the film, and how I might have corrected them:
SPOILERS AHEAD
(Note: L&S = Lucas & Spielberg)
Indy's age
Harrison Ford is older. Everybody is acutely aware of it, although he looks pretty good considering that he is nearly as old as my Dad. In the film, L&S should have lightly treated it early on, and then dropped the issue almost entirely. Maybe there could have been a running joke or two throughout the film, but that should have been it. As summertime escapism, what this story didn't need were constant reminders of everyone's ultimate doom, like the comment about how Henry Sr. and Marcus Brody were dead, and the speech about how they were at the age where life had started taking away more than it was giving. What a downer of a speech; I was depressed when it was over, which is exactly what a summertime movie isn't about.
Marion Ravenwood
What better way to remind us of Indy's age than to bring in an old girlfriend as part of the cast. The only reason Marion's character is even in this film is to confirm Mutt's parentage. Other than that, ask yourself if there is a single thing she did in this movie that helped the plot along in any way (hint: there isn't). L&S didn't give her a single line of interesting dialog, and she didn't provide anything important to the plot. There must be a million more creative ways to reveal who Mutt's dad is, and L&S went for the one that is the most mundane. Don't get me wrong, Marion also looks good for her age, and everyone remembers what a saucy piece of tail she was in 'Raiders', but in this movie she was just dead weight and a constant reminder that at her age she should be knitting sweaters. During one of L&S's script review meetings, her character should have been cut.
Mac
Mac is another character that should have been cut as he doesn't provide anything that makes the movie more interesting. He didn't provide a single line of memorable dialog. He didn't do anything to help the plot along other than drop those little homing devices that helped the Russians stay close on Indy's trail. His death (if that is what it was) was stupid and unrealistic for any character, no matter how greedy they might be. It was unbelievable that Indy would trust him after the initial doublecross. The only way that I see this character working is if he had perished in the early warehouse scene; this would have been a good way to refresh our memories of the 1950's mindset that said that anyone, even a close friend could be a commie spy in disguise...
Mutt
...which brings us to Mutt. I thought Mutt's character was interesting in the first half of the film, but then his parentage is revealed and from that point on he wasn't given a whole lot to do. From that point on, some time should have been devoted to building and redifining Mutt's & Indy's relationship, but it just didn't seem to happen. At the end of the movie, did Mutt treat Indy (or vice-versa) any differently than at the beginning of the movie? 'Crusade' had a touching moment or two between Henry Sr. and Henry Jr., but I didn't see anything like that here. Wouldn't you want to get to know the Dad (or son) that you didn't know you had?
What I think should have happened with Mutt's character would redefine a whole lot of the movie and make it a whole lot more interesting. Mutt's character should have remained mostly unchanged, except that it should have been combined with the Mac character in the following way: Mutt should have been the double agent. This would provide a several things: 1) it would have created the plot device that kept the Russians on Indy's trail 2) anybody, anybody can be a commie spy, and 3) it would provide Mutt a golden opportunity to "repent" and reconcile with Indy. I can easily imagine a scene at the end of the movie where Indy feels betrayed by his son, yet because of his fatherly love chooses to risk his life to save Mutt (who would otherwise die some gruesome death).
The Entourage
I go to see these movies to see Indiana Jones, and maybe a sidekick. What we have in this movie is Indiana Jones and Company. All the extra "good guy" characters are extra baggage that slow things to a crawl. Marion, Mac, and the Crazy Guy (whatever his name was) do nothing to make this movie more interesting. They should all have been cut from the script to make it more streamlined. Then the audience could focus on Indy, the comic relief sidekick, the bad guys, and the plot.
The Aliens
Unlike a lot of people, I think the concept of aliens in an Indiana Jones movie not only could work, but could work extremely well. The problem is in how the concept was executed. The sense of wonder that these movies usually have was shot in the foot early on. The plot's most amazing revelation is that aliens exist in Indy's world, and unfortunately this was revealed extremely early in the film in the warehouse scene when the alien corpse was shown. This proof of the existence of aliens should have totally been saved for one of the final scenes; up to that point, there should have been clues and hints that this was the case, but no actual revelations. L&S gave away their surprise too early and therefore didn't allow for any suspense to build.
Also, in keeping with the 1950's mindset, the aliens should have been hostile, and not some namby-pamby gatherers of knowledge. There were very few "saucer men" movies in the 50's where the aliens were benevolent. The backstory could be something about invaders that were miraculously overpowered by ancient South Americans, and sealed in a structure that was built to be their eternal prison. This would allow for an amazing confrontation scene at the end where the commies unwittingly loose the aliens, who would spectacularly destroy the commies before somehow Indy saves the day.
The Soundtrack
Back in the day, I used to like the soundtracks almost as much as the movie itself. That might be the reason that to me it seems like this soundtrack is completely recycled. I don't recall hearing a single theme that hadn't already been used in one of the previous 3 movies. I understand that this is a device used to remind me of the other movies, but that really isn't something I need. Most people understand that this is a sequel, and they've seen the other ones.
The Action Scenes
I don't have any suggestions for changes to the action scenes, but they are badly needed. I thought most of the action sequences were silly, ludicrous, and unbelievable, unlike the previous movies where they were silly, ludicrous, and yet I could somehow believe that they could actually happen. I blame this on over-reliance on CGI. In particular, the "ant" scene and the "Tarzan" scene were cringe-inducingly bad.
CGI animals
CGI dinosaurs work because I've never seen a real one, and anything that is even remotely well-done is believable as a result. But I've seen real prairie dogs, and I've seen real monkeys. Believe me when I say that I can tell the difference. Once again, this is just another component of this movie that destroys the suspension of disbelief.
...and finally, a plot change
The whole atomic bomb scene at the beginning didn't add much to the plot, other than to show off some cool CGI. Think about it: Indy escapes from the warehouse, there is an overnight break in the action, then he stumbles into the test site. From that standpoint, how does the atomic bomb scene have anything to do with the main plot?
What should have happened is this: near the end of the warehouse scene, the Americans arrive back on the scene with reinforcements and a battle ensues. Most of the Russians (especially the key ones) escape, but Indy is captured by the Americans. He is immediately suspected as having aided them, and thus is labelled anti-American (from the interogation scene, you get the feeling that L&S tried to establish something like this). He escapes from the Americans somehow, and spends the rest of the movie in a quest to clear his name (maybe by reacquiring whatever it was that the Russians stole). This would do a few things: 1) it would give Indy motivation for the rest of the movie, 2) it would add the Americans as another "hostile" force trying to "get" Indy, and 3) it would allow for a good wrapup at the very end where Indy is cleared (instead of the lame wedding scene).
Just some thoughts.