Even though some changes would have bigger impacts ...
The Motion Picture-Not make McCoy instantly-suspicious of Spock's loyalties or just reduce the length of the entering the cloud sequence.
The Wrath of Khan-Not a big deal but probably have some better, more convincing explanation for why there were survivors, but Kirk could find them, than just they managed to beam away and Kirk followed them. Or yes make the code, or the announcing of it, less obvious.
The Search for Spock-Keep Alley as Saavik and her portrayal more like in
II. Or make the battle with the Klingons a little longer, the
Enterprise not so instantly-crippled.
The Voyage Home-Just one thing would be minor but some better depiction of time travel effect or cut the line "Everybody remember where we parked."
The Final Frontier-Either cut the line "Hold your horse, captain" or make "God" in the end more of a threat to Kirk (or maybe make the threat to Kirk at the end something else).
The Undiscovered Country-Reduce Chang's Shakespeare-quoting/hamminess.
Generations-Make the crew seem more urgently concerned that LaForge was kidnapped or have Picard and Kirk be more reluctant to, a struggle to, decide to leave the fantasy.
First Contact-Probably have a scene of Riker again convincing Cochrane, after he panics, to go through with the mission, or maybe cut down on the Cochrane drinking/old rock n roll humor.
Insurrection-
show Riker convincingly persuading the Federation Council to give up or at least delay the plan, though runner-ups would be including the reason for Worf temporarily rejoining the crew or no Picard/Anij romance.
Nemesis-While a whole different story would be best, for just one change, no B4. A young evil Picard twin at least had potential, having
another evil twin (especially for Data who's already had one that is here ignored) was a whole worse level, B4 felt so extraneous and annoyingly forced in and pointless (and Data's story could have actually worked better without him, just being impacted by seeing and thinking about Shinzon and maybe remembering Lore). Bonus if it kind of cheats in that if no B4 probably no dune buggy scene also

.
09-I would have preferred that Amanda didn't die but the biggest would be not have Spock in the end favor revenge.
Into Darkness-Make Marcus less of a maniac-mustache-twirler, probably less of the main villain at all even if he did betray and anger Khan. Or avoid Kirk dying and being brought back to life.