I've been holding off on posting this wall of text, but bare with me. This is essentially a run down of everything I would change in the TMP edit to make it move faster.
Original Runtime: 02:11:52 (Including opening and ending credits)
New Runtime: 01:37:03 (not including opening and ending credits.)
Any scenes that are skipped over were either completely unedited from their original form, or had such minimal editing that they do not need to be referenced.
Remove the opening overture.
Cut down the opening sequence.
Particularly the overly long reveal of Epsilon IX. Location isn't worthy of this much focus. Tighten up some of the editing in the Klingon battle.
Remove Spock/Vulcan scene entirely.
There is nothing in here that contributes to the story
at all. Literally
everything the scene tells us is also dealt with later when Spock arrives on Enterprise. Now Spock's sudden appearance helps elevate the excitement of the events taking place.
Remove San Francisco/Starfleet Command entirely.
Go right to an establishing shot of Earth/Orbital Office. This is an extraneous scene that introduces a character solely to kill him off later.
Trim Office Complex sequence.
Again, we don't need fifty overly long shots of the model, no matter how awesome it looks. Rework the office scene to be just as heroic an introduction for Kirk as the SFC scene. Now he literally
beams into the movie. 
Reduce the size of the approach/fly around Enterprise.
Using the dialogue between Kirk and Scotty to resequence the events. Keeping the sense of awe, without dragging it on several minutes longer than is needed. The scene should be about establishing Kirk's lack of recent star time, and reintroducing the audience and Kirk to The Enterprise. Less is more.
Remove the transporter accident.
Kirk's lack of recent experience is discussed on the travel pod, with Decker in engineering, and culminates in the wormhole/discussion in Kirk's quarters. This scene is just an excuse to horribly murder a character who did not need to be in the film to begin with.
Remove the aftermath of the transporter accident.
It can be inferred that Decker's reduction to XO puts him in the science officer role and whoever would have done that job originally is down in one of the science labs.
Remove the silly Ilia nonsense.
Just trimming the dialogue so that the emphasis is on establishing:
A. Decker and her had a relationship.
B. There's a building tension between Kirk and Decker.
Take out Uhura's "Deltan" emphasis. Sulu/Chekov's doofy reaction shots, and the line about Ilia's oath of celebacy. Scene moves a little faster, and has much less awkward in it.
Remove the entire recreation deck briefing scene.
(I know!
I KNOW! Just stay with me here.
)
Chop out the goofy "I ALMOST MISSED THE DOOR" scene from leaving dry dock.
Loses the beautiful shot of the Enterprise with the sun rising behind it unfortunately, but the scene flows just fine
without it. We get
plenty of beauty shots of the E in the film. We can afford to lose some of these.
Insert a newly created scene between leaving dry dock and the wormhole sequence.
The Enterprise receives a signal from Epsilon IX. Sequence ends with stunned reaction shots of the crew as Epsilon IX is digitized. Transitions into Captain Kirk's log. Now with a bit more sense of immediate danger playing on things.
This scene is composed of editing the briefing footage into the bridge view screen (using several angles from other scenes in the film to give it less of a static feeling) and reaction shots cut from other sections of the film.
Wormhole sequence is left mostly unchanged.
Reducing some of Chekov's hammy slow motion performance, and taking out a shot of Ilia awkwardly bouncing in her seat. Shortens the scene and makes it play faster. I also think some music from one of Goldsmith's other scores would be good for this sequence. TOS almost never did a sequence like this without some bombastic music going with it.
Recut the scene between Kirk/Decker/Bones with Spock's Shuttle approaching.
When Decker leaves, transition to show the shuttle mysteriously approaching. Come back for the second half of the discussion, now have a much shorter section of the shuttle docking.
Scenes play much faster and with more energy this way. (And a heightened sense of mystery is added to the second half of the Bones/Kirk discussion.). Also, this edit excises Decker/Ilia melodramatic romance. We still get their history together from the rest of the film.
Remove the "sit down" nonsense in the lounge scene.
Kirk ushers the two men to sit down after the opening dialogue, and then after Kirk points out to Spock that he broke the Kolinahr by reupping with the crew. Spock then sits down, taking the point. No need to have Kirk repeat himself 50 times and unnecessarily drag out the scene.
Remove the "I can stop his pain" nonsense.
It never goes anywhere in the story. This really feels like a vestigial holdover from when the script was intended as the pilot for P2. Establishing character traits/abilities that never pay off.
Reduce cloud penetration sequence.
Make it about the characters reacting and not the visual effects. The line from Spock about the patterns being unrecognizable is good. There's a couple of decent reaction shots of the crew, but a lot of the FX just serves to drag the movie to a halt and it does not need to be this long to convey the size of V'ger's protective cloud.
Reduce V'ger Flyover.
Using the dialogue between the character's to rebridge the sequence you can cut this one virtually by 75%. Mostly by trimming shots. Some can literally be cut by half their length and you lose
absolutely nothing.
Trim bits of the Probe sequence.
Remove Kirk reiterating what Decker already said about not interfering. Remove Spock smashing the controls. Instead make it look like Spock ATTEMPTS to interfere with the probe and get's blasted for it. Remove one of the more awkward Decker shots right before Ilia is digitized. (His acting looks very contrived in one shot.)
Remove the "jetpack tutorial."
Start the scene with Spock recording his first message to Kirk. Spock Walk scene is perfectly fine as is.
Spock laying on the operating table in sickbay
Cull the pullback before Chapel comes into frame and sticks that thing into his ear. It's just gibberish dialogue. Cut from Spock on the table to Kirk and Bones looking at the monitor. Then Spock chuckles. Trim out the excessive "SPOCK! JIM! BONES! SPOCK!" Nonsense. Kirk grabs Spock's shoulders and Spock comes back around. Again, staying on point here. Recut the rest of the sequence to remove Kirk's one-way conversation with Bones. Kirk says he needs Spock ready to go back to duty and then talks with Chekov. We already had exposition about V'ger, we don't need Kirk to repeat it to us again.
Micro edits and trimming to the sequences that follow.
Mostly carving out the dead air that seems to exist. Kirk's "V'GER...V'GER!" to Ilia. Making the Ilia probe more insistent about Kirk revealing the information. Also, cut down the time it takes the Enterprise to fly through the flower-hole-orifice-of-metaphors.
The majority of the final sequence at Voyager can be left unchanged.
It all works pretty swimmingly. All the major arcs come to a close nicely. Mostly just trimming a shot here or there to keep things moving at pace.
It probably reads like a butchery to some folks, especially big TMP fans, but this isn't really conceptual. I've made these edits, and although they're very rough and need some finesse, they can work. They help to make TMP much closer to the feeling of The Original Series, and get rid of a lot of the dead weight in the film.
(or maybe even more near to 600)
