I prefer the theatrical cut. It moses quickly and none of the missing scenes are - actually - missed. By me. Their loss does the film no harm at all.
The original video version adds the cheesy "Scooby-Doo" ending with the Klingon unmasking, which makes absolutely no sense at all (why put a starfleet guy in a rubber mask, sit him with the Klingons, then have him get up and walk to his assassination position instead of just sending - a real Klingon?), the torpedo room scene (with the really awful, totally out of character, "Klingon bitch" line from Scotty) is ruined by the wobbly wall when Valeris slides down the fireman's pole (is there no end to the idiocy of this scene?). And the "clean their chronometers" line is cringeworthy ("let's put all our worst dialog back in!"), as is Col. West briefing the president on a secret rescue plan in front of a Romulan. All of these scenes were well chosen when cut and only make the film slightly laughable when reinserted.
The Director's Edition is worse, with Meyer adding the black and white flashback footage into the mind meld scene because we're too stupid to remember the names of characters we saw an hour ago. Not to mention the "BONNG" on the soundtrack behind each reveal. The only thing I liked about the DE were the alternate shots and angles not in the Blu-Ray version (although I do remember the McCoy close up in the theater).
Theatrical version all the way. But you'll find a LOT of people love the video version. So there ya go.