Data Holmes -- Why get rid of the "space walk" sequence? I think it helps maintain interest by getting the story a little less shipbound, and also plays quite well with the ambiguity of Spock's motives.
To be perfectly honest, I cut it to allow for the Klingon combat sequence at the end.
Your conclusion is definitely an improvement over the OP's, in that it ties the action sequence into the climax rather than tacking it on afterwards. But I still think it would feel out of place, too obviously shoehorned in for action-lovers. The Klingons would need to be more involved in the story as a whole for them to belong in the climax. I know a lot of Trek fans want to see some action on the big screen, but TMP really is not meant for that. You may as well start fresh with a story that actually lends itself to action.
I like a twist ending, but also like one which is still connected to the story. I thought a klingon ship showing up at the end and trying to claim V'Ger as klingon property was an interesting twist.
As I said before, I was perfectly happy with the climax of the main story, but I thought the character arcs just sort of petered out. With that in mind, here's my TMP "fix":
First, rip off the only good thing Generations did with Kirk: "Your place is on the bridge of your ship."
Have that moment come at the end. The Enterprise has been brought to the centre of the cloud, and a team has to go out and meet V'Ger in person. Of course Decker wants to go -- Ilea's fate will be decided there. But Kirk steps in and tells him that whoever goes out there is likely to die, and the ship needs its captain.
Now we get a two-for-one emotional climax. Decker needs to accept that his responsibilities outweigh his lost love, and finally say "goodbye" to Ilea. Kirk needs to give up the Enterprise and leave the ship knowing that, whatever happens next, he'll never be in command of her again.
Once the torch is passed, it all plays out as before, except that it is Spock who merges with V'Ger. It's at least as fitting this way; they both have what the other most desires. Nimoy wanted out of the franchise at that time, anyway, and TMP was always a more Spock-centric movie than TWoK.
Kirk returns, but doesn't sit in the chair again. Decker takes her out, and Spock gives us our closing voice-over just as in TWoK. I'd also let Ilea-the-probe survive the whole experience, giving us a "curious android" character to take Spock's place as the resident alien (at least until the inevitable Star Trek II: The Search for Spock).
I think it'd work quite nicely, if we're letting ourselves change the trajectory of the following movies as well. I'd like to have some larger role for Decker once he takes command, just so that we can actually see him do something now that he is captain. Maybe something as simple as making the choice to brave the "buffeting" of V'Ger's transformation long enough to save Kirk and Ilea.
Nice. I like what you did with the ending better than mine, actually.