The theatrical cut is missing a few great Spock scenes, but it's not a movie-breaking loss. The biggest issue really between the director's cut and the theatrical cut is the pacing. The film already looks fantastic. The extra gloss given by the new effects is just an added bonus. The pacing of the theatrical cut is just way more sluggish, but I suppose if you haven't accidentally broken the fast-forward button of your controller, then there's not much of a problem anyway.
Personally, I feel the pacing of the theatrical cut is far superior and fits the mood, style and overall intent of the movie with grandiose aplomb. Yes, it has a slow pace, so what? I love the awe-inspiring, epic and beautifully executed "pace" for what it is - just as I enjoy the radically disparate and livelier style of Trek '09 for example. I feel the DC was an attempt to alter the film's original feel due to the endless parrotlike "slow Motion Picture" whingeing, bleating and whining over years. And yes, I am aware Robert Wise was at the helm for the DC.