My favorites are Wrath of Khan and The Motion Picture, in that order.
Wrath of Khan is just kind of a perfect movie, and I like the pacing and atmosphere of the Motion Picture. It has a kind of 2001: A Space Odyssey vibe. To me, at least.
4 was fun, but I detest The Search For Spock. Even as a kid I thought it was dumb to resurrect him. The rest are so forgettable I've forgotten them.
I do consider myself a Star Trek fan, but first and foremost I'm a good story fan. I don't have a problem with chucking the stuff I don't like in the bin. I don't have to like everything Star Trek to love Star Trek.
The amazing thing about TWOK is that it shouldn’t work. The entire plot is built on one coincidence and contrivance after another. Chekov just so happens to find Khan by accident, and Khan just so happens to have mind-controlling creatures which allow him to steal the
Reliant, and then Khan goes after Genesis, which just so happens to be the creation of Kirk’s ex-girlfriend and son, and then Khan goes after Kirk, who just so happens to be taking the
Enterprise on a training cruise at the exact time when Khan escapes from exile.
Yet, the characters work, the action and suspense work, the themes work, and the “emotional logic” works. So…yeah. Perfect movie.
Whereas TMP has a solid (albeit “The Changeling”, rehashed) plot, but widely misses the mark on “emotional logic”, because it feels so cold and out-of-character.
I’ll also strongly defend TSFS. Yes, the plot is thin, contrived, and full of issues. Yes, the movie is basically connective tissue between II and IV, with the primary goal (for good or ill) being the resurrection of Spock. But, man, when it works, it works really, really well. Like TWOK before it, it really plays up the passage of time and the characters’ relationships. Kirk stealing and destroying the
Enterprise to help his friends is something which capitalizes on 20 years’ worth of history, and would not work without the weight of all those years behind it. The “emotional logic” works, even when the plot doesn’t. That final, intimate scene between Kirk and Spock (“Jim. Your name…is Jim.”) has more weight and resonance than anything in TMP.
I think that there are two kinds of TOS fans: Gene Roddenberry fans and Gene Coon fans. Roddenberry fans love the sci-fi procedural aspects, technology, and utopian ideals, whereas Coon fans love the characters, the interplay/banter between them, the personal drama, and the humor. Early TNG, when Roddenberry was in charge, is basically in line with “The Cage” and TMP: Less personal, more procedural and high-concept.
TMP is smarter, cooler, and more Roddenberry. TWOK/TSFS/TVH is much warmer, funnier, more personal, and more Coon.