When Khan fires a warning shot at the Enterprise, there's a quick cut to sickbay, then back to the bridge in the movie. There was actually a scene there where David leaves sickbay and Carol helps ready sickbay for wounded.
The "final" Kirk/Spock scene in Wrath of Khan is one of the finest in the entire series. Having Kirk sit there in silence as his friend dies in still heart wrenching.
The script has Saavik jump in with news to punch up the scene, but I'm glad it wasn't used - this is a solemn moment, and it needed to stay between Kirk and Spock.
So with the movie over and some of the changes annoted, there are a some things there that absolutely should hae been removed (the dumb bastard joke and some on-the-nose moments), but some things I'd like to have seen kept (Saavik being given a more "young leader in training" role).
Saavik in the movie comes across as just a new character, and in the script she seems to be set up as a replacement for Spock in future sequels. I also like that there is the BEGINNING of a David/Saavik relationship, and that it's not capped off at the end. Again, the feeling of setting something up for future movies.
This is the only draft of Wrath of Khan I was ever able to find, which is the Nick Meyer shooting script so sadly I can't do a comparison like I did with ST:TMP. If you have any of the early drafts, I'd love a copy/loan of them so I could do that comparison. Wrath of Khan also has an interesting (if much less volatile) history to its scripts. :)
Most of the Mutara Battle is exactly the same in the script as in the movie. There is one cut concept though. The child we see at the beginning of the movie, is shown as the Genesis device starts up. Again, a little on the nose.