It's amazing how wide ranging the storytelling was in the first six Trek movies, and now bland it's been since then.
TMP - V'Ger was arguably an antagonist, but misunderstood, not a villain. Epic stakes to the conflict, since Earth was in danger.
TWOK - Khan became a classic villain, but the actual conflict of the movie is personal and small-bore. Genesis Device or no, there's no real evidence that Khan wants to do anything other than fuck Kirk up. And of course there is the underlying theme of growing old and changing throughout the movie.
TSFS - There is a villain (Kruge) but arguably until the end of the movie it takes a backseat to...well...see the movie title. Stakes are arguably a bit higher, since Kruge wants to use the Genesis Device as a weapon, but there is no direct threat to the Earth or the Federation during the course of the movie.
TVH - While the probe puts Earth in existential danger, it's basically just the MacGuffin to set up the story. Certainly not an antagonist - the movie is a comedy and lacks a real central antagonist.
TFF - Not a good movie, but it should be noted that while Sybok serves as the film's antagonist, he's actually not a villain, and the side plot with the Klingons is totally forgettable. Arguably the end of the movie had pretty high stakes if "God" escaped, but that wasn't the tension of the film, so I don't think it counts as epic stakes.
TUC - Chang was an interesting, complex antagonist, arguably a villain. But it was a strange movie structurally speaking, because if the heroes lose, it's basically status quo - the fight is actually to improve things, not keep them the same. Also it of course involves aspects of murder mystery and political thriller, which is not something movie Trek did before (and hasn't really done since)
Then, the movies start going downhill structurally:
GEN - Picard (and Kirk) must defeat Soran to save Veridian IV, a pre-warp planet. Oh, and the Duras Sisters show up for some reason. Small-ish stakes (planet we've never heard of).
FC - Picard meets "his Khan" in the form of the Borg Queen. The gang must all team up to reset the timeline and save Earth. Epic stakes, classic personified villain which arguably began the process of ruining the Borg. IMHO the stuff with Cochrane on Earth worked much better because it was just seeing the rest of the cast working collaboratively to overcome a problem.
INS - The TNG crew travel work to save 300 hippie squatters from their evil relatives. Horribly forgettable villain in the form of Ru'afo who wasn't even needed - it would have been better as a moral quandry internal to Starfleet, as a "man versus himself" plot focusing on Picard's conflict between duty and justice. Though that's more TV Trek than Movie Trek.
NEM - Picard meets "his Khan" for a second time, this time for realz. He's like an evil clone! And he wants to destroy Earth, just because!!!
ST09 - Nero destroys Vulcan, and he will destroy Earth too, because he hates Spock that goddamned much.
STID - Khan literally comes back, though the movie is muddled whether he or Admiral Marcus is actually the antagonist. Marcus is the one threatening Earth with war for his own purposes, while Khan just wants to go home. Yet the film plays to the personal animus between Khan Spock/Kirk. I think it would have worked a lot better if Khan ended up being an ally throughout the film, as it would have subverted expectations rather than seeming like a shallow TWOK clone.
BEY - Krall was a sucky generic villain until the end of the movie when we finally discover his motivation. I don't think the movie could have worked structurally without him, but they shouldn't have been so wedded to the "twist" that they kept us in the dark regarding his true goals until the end. At least the stakes were modestly lowered after three movies in a row where Earth was in serious danger.
Massive changes in Kirk's time period already which will amplify as time advances. 
