Yeah, throwing kirk off the ship wasn't at all justified.
And then there was Zulu with the Katana. (In case it wasn't mentioned yet: Takei insisted on a rapier for "the naked time" since he thought a katana would be too cliché)
Oh, and while they hinted that "They can die, the timeline has shifted" they should have followed throught with at least killing a minor major character. (Vulcan doesnt count. It's a planet. It's victims are faceless. And Spocks mum was too marginal for me to buy it either. Janice Rand or that irish guy would have been a good idea)

Besides that i found it oddly fun. Maybe because i was prepared for anything after Nemesis and Insurrection, maybe because it really was. Plotholes? gotta agree... its star trek. It wouldnt be star trek without some major plot holes.

Oh: And Uhura and spock? I think you are mixing up Uhura and Nurse chapel.