I’ll die on the Spock’s Brain hill any time, but even I can’t defend And The Children Shall Lead.
Worse still for me is The Way To Eden. Talk about a counter-cultural show pissing on the counter-culture. I do not reach and I’m good with that.
Still, hardly controversial.
15 episodes of TOS that I think are worse than Spock’s Brain:
Mudd’s Women
Miri
What Are Little Girls Made Of
Operation: Annihilate
Catspaw
The Alternative Factor
Wolf In The Fold
And The Children Shall Lead
The Way To Eden
Is There In Truth No Beauty?
The Paradise Syndrome
That Which Survives
The Mark Of Gideon
The Savage Curtain
Turnabout Intruder
Even then there’s only three of the above that I’d struggle to sit through. Even when it was off its game, TOS was still the best game in town.
I disagree with nearly all of your choices, especially...
"What Are Little Girls Made Of?" - The best and most sinister exploration about the implications of AI, and the loss of what it means to be human, which cannot be replicated by any artificial being. Star Trek has never addressed the subject in so powerful a degree since--yes, that includes all things Data on TNG.
Operation: Annihilate!" - Always breaking new ground for filmed sci-fi, the threat of creatures (appearing like large, pus-covered scabs...yes, that's disgusting) acting individually, yet part of a massive, galaxy-spanning collective (and drawing its strength from said collective) was and remains one of the most frightening threats seen on any ST series. Add the method the parasites used to control victims (injecting tentacle-like tissue into the nervous system), and quite obviously Kirk's loss, and the ever-growing bond between the Big Three, and season one's finale ranks as one of the series' best hours.
"Mudd's Women" - Prostitution and a version of mail-order brides existed in the 60s, continues to this day, and despite the Federation believing it had overcome such despicable, abusive practices, it will exist in the fictional 23rd century. How "evolved" Starfleet officers had difficulty dealing with a practice they--apparently--were not too familiar with (and had no real authority to end) was part of this episode's strength, and--contrary to TNG-era Roddenberry's claims--the TOS future did not paint a picture of humanity (or any other species) overcoming many of the human failings common to the 20th century.
"The Paradise Syndrome" - if
"City on the Edge of Forever" did not sell audiences on the idea of Kirk's fate being to never find permanent love, this 3rd season romantic tragedy should have been the convincing argument. "Kirok" was naturally acclimated to the life with Miramanee, a woman the polar opposite of any he knew up to that point (or the worlds which shaped them), but that was only possible because the man within--Kirk--longed for that kind of existence and love (as he admitted to Spock and Bones in the teaser). That said, in the end, its almost as if
his own existence (in the life and service to Starfleet) stands in the way of his chances for love, making Kirk one of the better crafted tragic heroes of sci-fi.