I absolutely love the Great Movie Ride, and it's probably my favorite ride at MGM. Of course, I'm not a big thrill ride guy, so I kind of shirk Tower of Terror and Rock n' Roller Coaster.
That being said, there are definitely scenes that cannot be changed, because they are classics. Just because the movies aren't all recognizable, doesn't mean they should be removed. It would betray the integrity of the ride. It is supposed to celebrate the great classics of cinema history, and taking out these things to add punch to the ride would be akin to putting characters in the Jungle Cruise.
Looking at a list of films in the ride (which when you look at it listed is much shorther than I expected) I can see very few films that you could sacrifice: Alien and Fantasia being the most prominent candidates. The Fantasia scene should really be just torn out and replaced with something else. The only reason I can see for the way it is now is so people can tell others the factoid about the space originally being planned for the Tornado. Now, all these years later, it should be changed.
While Alien is not necessarily a classic in the sense of these other films, it is a very popular film and series, and the experience is one of the high points in the ride. This could be replaced by a Sci-Fi section akin to the Gangster and Western sections, which would include movies such as Star Wars, Alien, Close Encounters of the Third Kind, A Trip to the Moon, 2001:A Space Oddesy, Metropolis, and perhaps the Star Trek movie. Actually, upon further thought, having the whole set replaced with a similar 2001: A Space Oddesy scene would be nice, but it would probably be better to do all them.
The large Fantasia section could be replaced with something better, and could perhaps become home to more than one film.
As for additions to the ride, I think one of the first priorities would be to include a movie that should be here. I think it is unbelievable that the movie that is lauded by many to be one of the greatest, and was the greatest movie of all time on AFI's list: Citizen Kane. It doesn't have to be much. Perhaps it's dark, and you hear his last word "Rosebud", which our CM explainins can mean only one thing. He then presents Citizen Kane to us, and we see the iconic scene in which Kane gives his grand speech in front of a large poster of himself. That's all we need, and you can even drop the Rosebud part if you want to make it even smaller.
The Godfather films deserve a place in a classic movie ride, but it could be debated that the films are not in place at Disney. Goodfellas is also a classic. I may be having a little brain failure here, but Gone With the Wind isn't featured, is it? I would absolutely love to see the "Paradise" scene from Willy Wonka and the Chocolate Factory. You've got Mutiny on the Bounty that you can add. The scene in front of the flag in Patton would be a great dramatic scene. West Side Story is a great movie. We can't forget Rocky. Maybe Easy Rider.
Now, I don't know if they can use movies featured in Universal, but Jaws is a welcome addition. Terminator would also be a great addition to the Sci-Fi section.
What about a comedy section? M*A*S*H is a classic, but falls under the same problem that I mentioned with the Godfather. Movies, actors, or characters for a comedy section could include Dr. Strangelove, Charlie Chaplin, Abbot and Costello, Laurel and Hardy, The Marx Brothers, Monty Python and the Holy Grail, the Three Stooges, the original Pink Panthers, Tootsie, Airplane!, Annie Hall (yes, I remember the Woody Allen comment from earlier), and Animal House.
There's also horror. I mean, the little section with the temple definitely has horror elements, and we could see the Mummy in this scene (the classic mummy, not the one from the recent movie of the same name). With a little reworking of the scenery, we could also see Dracula, Frankenstein, the Wolfman, and the Phantom here. If a new section were built, we could also get a peak at Rear Window, Psycho (maybe too much for Disney), Polstergeist (same), and Jekyl and Hyde (imagine a scene where an AA Jekyl addresses the audience, takes his concoction, and then falls to the ground, a CM dressed as the monstrous Hyde popping up and taking over the tram from the host CM, making up a third scene to complement the Western and Gangster sequences). The major problem is that recent horror films, and the characters therein, have been highly graphic, sexual, and gorey, and appearance of their characters may be frowned upon. If these movies are written off, there is no Michael, Freddy, Jason, Screamface, of Leatherface, as well as anyone else I might be forgetting. The scenery could be a dark town with dense forest surrounding it (scenery would include the Amityville Horror house).
If you want to change the jungle scene, you could also make this a multiple movie area. The Predator could be watching us from above. A few characters from Apocalypse Now could be not too far off (along with the phrase "I love the smell of napalm in the morning" being uttered when you walk by). Alec Guiness and a few Japanese could be looking over plans as we see the titular bridge over the River Kwai being constructed in the background.
A military scene akin to the other mixture scenes could include M*A*S*H, Patton, Apocalypse Now, John Wayne again (although I'm not sure if you want him featured twice), and Full Metal Jacket (DEFINITELY not making it in Disney, but one can dream of a censored Hartman AA telling me I will not like him).
Wow. I really go way too far when I start thinking about things. Anyway, that's a small sampling of what could be added to the Great Movie Ride. Of course, I would be insane to suggest all these things. Only two or three can be implemented, probably, but there's plenty to choose from.