Wrath of Khan hands down. After the letdown of TMP, TWOK was like a breath of fresh air into the franchise and exactly what a Trek movie should be and TMP was not. It gave us a lot of what fandom had be jonesing for in the lean years of the 70's, including realistic character development (the aging crew angle) and the first full-fledged space battle. It also gave us one of the most memorable and emotional plot twists in Trek history by the death of Spock. Even if one suspected it might not be a permanent state, no true fan came away from at least the first viewing with dry eyes.
TUC on the other hand was not a bad movie per say, but just more like what TWOK wasn't and devoid of a lot of its spirit. It was a good send off to the TOS crew and I liked that it bridged the gap between the TOS and TNG era by planting the seeds of the Federation-Klingon Alliance as well as the dramatic portrayal of how even in a utopian future, peace can still be a difficult concept to embrace and change, even for good, doesn't come easy for some. I also liked that after years of the first mention of Sulu being scheduled to command the Excelsior in various extended-universe and non-canon sources, we finally got to see it.
My only two somewhat constant criticisms have been the concept of the wide conspiracy that involved Starfleet members and the level of violence.
For the first, maybe my thinking had been clouded by years of viewing the Federation as this perfect construct and how I wish the future will be, but most likely won't. So, I did take issue with the idea of this vision being somewhat tarnished by revealing there were those that still were willing to keep the killing machinery going, either due to personal benefit or mistrust. I also didn't enjoy the revealing of Valeris being revealed the traitor maybe because I never liked her as a character as she just seemed uninteresting to the point when her deception was revealed, it was like "ho-hum". Having the original concept of Saavik returning and be the traitor would have been shocking and made the movie much better.
For the second issue that of the violence, while it's true TWOK pushed a lot of the boundaries of gore, particularly with its ear worm scenes, the Klingon assassinations really amped it up a level, giving us the first Trek film above a PG rating. While I have no issue with sex & violence being the staple of other forms of entertainment (though over-reliance on it shows lazy story creation), I never felt it should be part & parcel of Trek, even though it had been making creeping inroads (at least the bloody violence part) since TWOK. This is perhaps one of the biggest reasons I despise STD so much as well as the idea that was floated of a Quentin Tarantino Trek; as Star Trek should never be R-rated entertainment.
