In the Pale Moonlight doesn't deal with time travel. neither does The Best of Both Worlds, Mirror Mirror, Duet, etc. Now Yesterday's Enterprise is a top tier episode, easily Top 10 TNG, but I wouldn't put it at the #1 spot.
Thinking about it, and assuming you're not including movies, you're probably implying that The City on the Edge of Forever is the"best episode". To me The City on the Edge of Forever is third most overrated Trek episode after The Inner Light, a boring waste of time that is still somehow less bad then the original script but thats a low bar to clear. Its an episode I'll never rewatch unless for some reason I need to make myself simultaneously very annoyed and really bored. I mean I would rewatch it over The Inner Light or that horrible "Captain Sisko is a sci fi writer in the 50s" DS9 episode, but the bar is in the dirt at that point.
I pretty strongly agree with some of your takes here, but I'll note The City on the Edge of Forever is quite different from what this episode is doing.
The City on the Edge of Forever is a character drama like all of the best Trek episodes. It revolves around Kirk's emotional conflict between his love for Edith Keeler and his sense of responsibility to restore the timeline to what it should have been. Kirk is placed in an impossible situation between two awful choices, and he decides to not save Keeler's life because he understands in the end, duty overwhelms love. But it's still a choice - it's his choice to fix the timeline, as we know the bad timeline has already happened due to McCoy's actions.
In contrast, Pike has no real emotional conflict here, because he only realizes the decision before him like 10 seconds before the moment of his (in)action. He doesn't wrestle over anything. And although he feels some sense of duty as a Starfleet captain to stop a genocide (or at least, not allow his own ship's antimatter to be used to cause one), this is a pretty rarified intellectual issue. The bug people are not given any sense of humanity here. We don't have a humanized character to act as a stand in, as we do for the Martians. Pike presumes that maybe it's all a big misunderstanding and they aren't a senseless killing machine, but we're shown nothing to suggest that (hell, we're shown nothing to show them as killing machine either - we just are told). This would all have worked much better if the Commander's people were the ones on the fifth planet, and ended up getting blown up, because then we'd have a sense of dramatic pathos here.
But worst of all, unlike in TOS where they were trying to fix an alternate timelike "back to normal" here we have the strong implication of a causality loop. This completely lets Pike off the hook, because it's not a story of character agency, but "destiny." IRL, I'm actually someone who's very suspicious of the idea free will exists, but in a story focusing on a supposedly heroic captain, it really diminishes the protagonist.


