Having recently watched this on blu-ray, I frankly don't have too many problems with the theatrical cut, for what it is. Maybe a bit slow, but they were trying for the 2001 vibe.

Regardless, to me the biggest problem is that there is no real strong secondary story - I understand it is supposed to be about Spock coming back into the fold and coming to terms with his human side, as well as Decker and Ilia, but what the movie needed was a strong secondary conflict (ie. Decker acting more like his father and/or his crew helping him commit mutiny and taking over the Enterprise or something to that effect; V'ger wants to test the Enterprise, so reintegrates one of the K'tinga's - but to have a K'tinga hunt the Enterprise within the cloud as V'ger watched "after" ST2:TWOK would seem redundant and copied now).

I can understand the Borg angle, and frankly was kind of hoping at one point in ST:TNG that Q would have some part in destroying the Borg in BOBW part 2, as he would reveal that the Q was the evolved V'ger, with their mission not just to protect humanity but to test them. Maybe the machine world (Ix?) that found Voyager found other probes, and the Borg are simply a different tact taken to "merge with the creator" of another alien probe from a different part of the galaxy. Maybe the machine world's primary existence is like a flower, waiting to be pollinated with probes from alien races, whereupon it would send out a seed to merge with that race (?).

In the end, there was not enough character conflict, change and build-up, as the primary (and seemingly sole) focus of the movie was how the characters reacted to a cloud threatening Earth. Regardless, there is some fantastic imagery, and to see STAR TREK on the big screen for the first time (at 8 years old) left some pretty damn good childhood memories...