Leave Alien in but take out the Indianna Jones and the Temple of Doom sketch because that is the worst acting of the entire ride. Plus there is enough Indianna Jones already at MGM. Since they have rope there for the Cast member swing across that would be great place for them to swing from a pirate ship to another pirate ship if they put in POTC.
There is no "Indiana Jones and the Temple of Doom sketch." You may be referring to the scene with the greedy mobster/cowboy going for the jewel, but that's not related to Indy...except that it's near the Indy and Sallah picking up the Ark scene from "Raiders" (no bad acting in that, though; just a lot of heavy lifting!). But if it is the "Halt, unbeliever!" scene you're referring to, I'd probably have to agree with you most of the time. I love The Great Movie Ride (best attraction in the Studios, in my opinion), but the transformation of the "Halt, unbeliever!" guy into the original driver never works properly, as the fog never builds up fast enough to hide the person taking their cloak off. So, you're stuck watching a person removing a cloak, then screaming "Ta-da!" just as the smoke gets strong enough to envelope them. If only they could figure out the timing on that...
If I were to replace anything, I'd probably do something about either that scene (and just not change hosts at any point in the attraction), or I'd do something with that lame "Fantasia" scene. Every other scene is filled with great audio-animatronics and then we get to Mickey Mouse, who is just his usual cel-animated self. Audio-animatronic Mickeys already exist. How hard would it be to put one in? Maybe take it a step further and put in a number of Disney characters. A scene from Roger Rabbit, perhaps? There's a great mix of classic and new.
As for the "Alien" scene, it might be cool to update it to the sequel "Aliens." More characters, more aliens, more danger!
And then if I were to really have my say, I might request audio-animatronics be alternated with the film clips in the last scene too. I realize, though, that the last few years have seen a decline in the number of AAs in the Parks, but this attraction could always use more.