The cons on this cut for me are two, firstly the cut scenes and alternate scenes from the longer version. The alternate verisons of scenes from the theatrical version are much stiffer and I thing in some cases only placed in the cut for temp and not really meant to be used. For example, a medium shot for Bones is lecturing Kirk in Kirk's office you see a two shot of the men talking. The shot and the acting in the shot is wooden (the dialog in that scene I believe is "make your point doctor." "my point captain is that it's you that is competing" etc). In the alternate of that scene it's starts differently ("and another thing..." "get out of here Bones" "as ships doctor I am now discussing the subject of command fitness!" "make your point doctor.") that scene, and maybe two others I would add, as for the rest I would leave the cuts in place, including the Klingon battle, and the station distruction.
The second con is sound effects, while I feel more post production sound effects needed to be added, most of the ones added weren't that great. The alert sounds I the were aweful. As Star Wars has it's well known sounds (lightsabers, blasters, etc) as does star Trek. A well known red alert sound could have been used and would have sounded great. Why this was not done I can only assume either had to do with time or to do with givinig the film it's own sound. But the sounds are as much Star Trek as the actors, and we need to hear them!
So in short, if it were done my way, replace with and add some of the "longer version scenes (not most) and leave the trimms and effects as they are. And recreate a sound mix, a nice new 5.1 mix that mixes the sound and music better and adds fimiliar effects across the film.
Call it a "Director's Cut Special Edition" if you will.