When I consider TMP more I can envision the inclusion of a couple of short scenes that could have down wonders for the film without taking anything away.
Early in the DE version we see the scene on the bridge where one crewman questions Kirk's command by asking about Captain Decker. Uhura replies to it. Now if this could have been followed up in a later scene (perhaps in the rec room) where Sulu and Uhura are faced with a couple of Decker supporters and there is some real heat being generated. When it gets really heated Decker happens to come by and diffuses the situation by reiterating that while he appreciates their support he asserts that Kirk is indeed in command and he won't have anyone questioning it.
Now follow this up with another small scene between Decker and Ilia wherein he faces up to why he really left her behind on Delta. We can then see that Decker is really questioning whether he wants Ilia or a Starfleet career.
The scene in Kirk's quarters where McCoy challenges him could have been expanded a bit. This could have been a good place for McCoy to deliver a little exposition to clue the audience in on things that happened earlier and offscreen. It's a scene that should play out much like the similar scene in "Obsession" when McCoy challenges Kirk's obsession over killing the vampire cloud creature.
"Jim, you've been miserable since Nogura maneuvered you into accepting a promotion. This incident gave you the golden opportunity to turn the tables on him and get your command back, something you should never have given up in the first place. You rammed it down his throat and you'd rather die than lose it again, maybe even if it means taking all of us with you."
"Get out of, Doctor!" Kirk snaps loudly.
"Negative, Admiral. You'd better be sure your priorities are straight or you'll never again be the man you once were. The man you want so desperately to be again."
Something like that and then the rest of the scene could play out pretty much as it did.