Let's take the basic ideas of KOTCS, the basic story etc and try to make a better film out of it. My personal opinion is that the general ideas present in KOTCS are worthy, they simply suffer in execution. I think KOTCS had the potential to be an awesome film, on par with the others, it just wasn't done right. I'm fine with aliens in Indy myself. I'm fine with going that route. The general ideas presented are good, but they need tweaking IMO.
Here's my ideas on how to tweak KOTCS to put it up on par with the other three:
For me, if you:
-Retool the Mac/Indy storyline so it has more of an emotional impact. Give Mac a little more backstory to make his "double agent" ways more understandable.
-Focus a little more on Indy's age and the fact that he has NOTHING: No wife, no family, his father's dead, Marcus is dead, his country thinks he's a traitor. Accentuate Indy's sense of being alone--not to the point of melodrama--but to the emotional levels of TLC perhaps. He's a man without a family, without a country, who can't even trust his friends. A man who is becoming a relic in his own time as the autumn of his life comes ever closer. A more "Robin and Marian" feel in certain respects. Rather than have him tamed by age as KOTCS does, have him embittered by his sense of loss, his sense of betrayal, by the changing times. Not a bitter old man per se...But more a Lion in Winter. Still an anti-hero, just older, gruffer, a little more grizzled, more jaded perhaps. A man who is less impulsive but still willing to do what he has to do to survive. A weary old Cowboy weathered by changing times, loss and age. Not the family friendly old fogie we got, whose age is the cause of kids' laughter. No "Get on, Gramps." No jokey jabs at his age. An older man, but not a Grandpa per se. Think of the old Western movies with the old, rough cowboy or gunfighter. No "Indy is becoming his father" stuff. Maybe that can be touched on, but in terms of him becoming wiser and more careful--Not being soft.
-No prairie dogs or Tarzan scene. Nix it. No prairie dogs.
-His name is Indiana Jones. Not Henry Jones, Jr. Stop calling him Henry Jones, Jr.
-Make Oxley a character we care about. Give us more time with "normal Ox" rather than "Old nutcase Hippie babbling" Ox. Maybe if they really wanted to break from tradition, the prologue could've started off with Ox going on the search for the Skull and being captured. We'd see Ox before the Skull destroys his mind. We'd see that Ox is a man like Indy but more the professor side of Indy. A gentlemen grave robber. Sort of a friend who is the closest thing to Abner Ravenwood that we'd ever see.
-Have Indy participate in a gun fight, on a scale not seen since TOD or the Raiders bar scene, and have Indy kill a few people. Have a moment where it seems Indy is dead or done for. Perhaps Mutt steps up to the plate here and save his life in Mutt's one major action scene and something that shows him to have the moxy of a Jones.
-Have Indy participate in more action; Lessen Mutt's role in that regard. Make the Jungle chase the centerpiece action sequence of the movie ala the Truck scene from Raiders or the Tank chase in LC.
-Perhaps jettison "Mutt as a Greaser" completely or retool his character a bit; Make him harder edged or more original. Make him close to the real, brutal '50s juvenile delinquents you see in films like Sometimes They Come Back. Or have him be Indy's daughter rather than son on the extreme end of things.
-Get rid of Doom Town, or put something just as tense but more realistic in it's place.
-Retool the film from Marion's entrance to make that have more depth, more of an emotional sort of feel. A little more dialogue between them, a moment or two with them alone. We don't need a sex scene, just a little tender moment which echoes Raiders. Maybe Marion tending to Indy's scars, but he's older, the pain isn't as easy to bear. Or something where they have a delicate moment. Think of the tender moments between Henry II and Eleanor in The Lion in Winter. Two old hardasses at each others' throats who deep down never stopped loving each other.
-Make the Aliens a larger presence in the movie, if unseen. Unseen eyes ever watching. Eerie sort of feel. Think Twilight Zone-ish perhaps. Make the film have a creepy undertone and the Aliens have a slightly sinister presence. Sinister, but good, like God in Raiders. Think of how you KNOW something dangerous, dark and sinister lurks within the Ark and how it's treated with this eerie, mystical aura throughout the film until it's full power is revealed at the end
-Either eliminate the wedding or make it more believable. Make it clear how Indy's reputation is restored. Don't make him an Associate Dean. Just do something like James Bond where he gets his 00 back at the end. Have at least Sallah be present at the wedding or Short Round. At least some further connection to the original 3.
-Add another twenty or thirty minutes or so onto the movie to fill some of these issues out. This is Indy's last ride, right? We can afford 20-30 minutes more if it makes the film that much better.
-Shoot the film in a style similar to the first three. Less wide shots, etc. Sometimes I feel when watching it that the direction STYLE feels too modern; It does't feel at times like the hand of Spielberg. Certain shots just don't say "Spielberg" to me. The direction doesn't feel as tight as Spielberg's; Certain shots remind me of Lucas' style actually. A little better editing here and there. Have the cinematography be less "1950s oversatured look" and closer to the original film's look.
I have a rough idea both how to flesh out Mac's character and create an action set piece to start off the film. Have the prologue of the film be a flashback to say 1944 or something. Think Utah 1912. Indy and Mac are on a mission, to collect an artifact or something, as spies. Mac maybe saves Indy's life; we see their comraderie. Bridge it somehow to the Hangar sequence so it doesn't feel disjointed. Have the Paramount logo dissolve into something less stupid than a molehill. I repeat again: No prairie dogs.
The film should also have followed the trope of Indy going from the fire pan to the fire. What I mean is each thing he faces should be more dangerous than the last. It builds, with pauses for exposition in between. and builds again. In KOTCs, Indy faces his biggest threat (Doom Town) in the first 15 minutes and we never come as close to death with him again. The structure set by the previous films--A serial sort of feel, edge of our seat sort of feel--is broken here.
Films/TV shows to look at for reference: The Lion in Winter, Robin & Marian, The Misfits, Hitchcock's films, some of the darker 50's B movies, The Twilight Zone, The Man in the Grey Flannel Suit, The Gunfighter, The Man with No Name series.
If all of the above had happened, I believe we would've had a classic film on par with the other three.
But, submit your own ideas and tweaks and whatnot, please