I'd place it as my second favorite. From what I've seen(that movie list favorite thread comes to mind), most people will put UC in their top three.
Kirk a racist? Well losing a son doesn't help the sunshine and love feelings. He overcame it as a true hero should. Human anatomy alone is highly complicated, I see no problem with McCoy not knowing Klingon anatomy when the Federation has dozens of member species he's more likely to be treating first. He knew enough to briefly revive him regardless. I thought the Uhura scene was weaker because they yanked out books rather than used a computer to figure out what to say but that was more a early 90's thing than anything. As for Spock mind raping Valeris? I got to give a pass on that one. If he hadn't done that they still wouldn't know who the assassins and conspirators would be. So saving the life of the President and Chancellor rates above a few moments of discomfort for a non-repentant murderer and traitor.
I thought it was a good movie and a grand conclusion to the TOS story arc.