My choices:
ST First Contact: It's well-directed and has some terrific f/x, but without a good story those added bits don't hold up. The story is a retcon of the Borg, Worf and the Defiant come out of nowhere and not with the best crew on board given who the enemy is, what's Picard doing there in the flagship if Starfleet doesn't trust him, why does he break orders and all the Starfleet ships are quick to believe him so they all fire on cue -- and that's just in the first 10 minutes alone. Never mind the rest. Least of which is the Borg Queen. Alice Krige is awesome as the Borg Queen, true, but the Borg queen flatly contradicts the Borg's very premise so it was not easy to accept given every Borg story prior to STFC and how much even the most casual fan already know. Back to the first 5 minutes, even Picard disobeyed orders as a lame joke for us to laugh at, which "Insurrection" would later play straight. Barclay gets a nice shallow moment to devolve as a character into a caricature of himself as well -- he's used so much better in Voyager and had already made progress in TNG, so to see him as a disposable comedy act in an "event" movie... no thanks. It's a cast reunion shindig aimed at fans but isn't by any means a well-written movie event. Previous Trek films had continuity gaffes as well, but they're subtle (and very few) by comparison. (Do I dislike STFC as a whole? No, there are far worse movies. But on the storyline level, it's got problems. Lastly, did they get inspiration for looking at ships in the sky (where they look like dots) from "Blake's 7"?

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ST2009: It cashes in on name recognition, but offers nothing that Trek as a franchise holds unique, it's a caricature relying on the name and parodying a number of set-pieces than actually telling a story. Remember that 1995 comedy movie "The Brady Bunch"? ST2009 is in the same pastiche except it's not meant to be funny. Having said that, "Into Darkness" has a DS9-like quality regarding the double crossing and terrorism angles and to the point STID might be underrated in a couple of ways, and the pre-credits bit with the alien planet definitely had a TOS feel (despite the humor, which despite it all worked for me.) I've heard some good things about "Beyond" and am hoping to see that shortly.
Honorable mention: TVH. I loved the movie in 1986, but it set the stage for TOS movies' downfall with the insistence of comedy at the expense of depth. TVH was lucky that all the elements gelled and how the comedy worked with the plot, that usually doesn't happen. On the plus side, unlike STFC, TVH had a coherent way to get everyone back to their intended time period...