Over the years I'm leaning towards Plato's Stepchildren. Alternative is incompetently bad. (With lots of production issues.)
But Stepchildren is mean and unpleasant. And I don't like watching it.
Both of them are the hardest episodes to watch. It's easier to watch And the Children Shall Lead. (Spock's Brain isn't even in the running. It's fun to watch.)
Oh, and the end of Alternative (from when Kirk talks to Sane Lazarus at the end) to the last scene is really damn good. The rest of the episode is so unwatchable that I often forget that.
Going back to hating on Alternative: It just talks wrong. i can't explain it. It sounds like someone filmed a Gold Key comic. The words are CLOSE and certainly run of the mill sci-fi. But a lot of it isn't quite Star Trek. (See why Gene had to re-write everyone until they hated him?)
Space Hippies is in kind of the unwashed meh of Star Trek for me. But the end of that episode was both scary (the GRASS will kill you!) and moving. (Kudos, Mr. Nimoy.)
I should start a thread "What episodes of TOS do you not care about one way or the other." Oh, hello Miri!