This is where I feel there was a lack of thinking things through or something just turns me off the story as a whole.
"More Tribbles, More Troubles" - The original episode didn't beg for or need a followup. This was just lame.
"Mudd's Passion" - Harry Mudd isn't a bad character, but this story merely served to make the main characters look bad. This might have been salvaged with a thorough rewrite.
"The Terratin Incident" - I just couldn't buy into the shrinking people idea.
"The Eye Of The Beholder" - In many ways this was a variation on "The Cage" and an unconvincing one at that.
"Bem" - Not really a bad story idea, but the depiction of the colony being is just too stupid.
"The Practical Joker" - The Enterprise computer gets infected and becomes a pain in the ass. Hell, no.
"How Sharper Than A Serpent's Tooth" - A retelling of "Who Mourns For Adonais?" only with a winged serpent as a God. And just how did such a being make and develop all this tech without any manipulative limbs? I kept waiting to see the "guy behind the curtain"--so to speak--but he never showed.
"The Counter-Clock Incident" - The appearance of Robert April is overcome by the too bizarre idea of people born old and regressing into children as they age and...then?
For me one litmus test is being able to imagine some version of a given story happening in the live-action TOS universe.
"More Tribbles, More Troubles" and "Mudd's Passion" are both lame and pointless followup stories to live-action predecessors. Given a choice I would totally excise them from canon. But it is possible to imagine a rewrite that would make these stories passable. It isn't necessary to have tribbles bcome an oversized colony being when you can just inundate the
Enterprise again with regular tribbles. It's still silly and pointless, but it's doable. In "Mudd's Passion" it's more clearly a case of introducing nuance and not having the crew--particularly Chapel and Spock--behave so ridiculously. Perhaps find another way of introducing Mudd's potion into the ship's environmental system.
If you can rationalize a somewhat credible way of shrinking people in size then you can make "The Terratin Incident" work.
"Eye Of The Beholder" doesn't grab me, but it's still feasable.
"BEM" as visualized is cringe inducing. Rethink Bem as colony being and this might work.
I find "The Practical Joker" ridiculous, but having the ship's computer infected with a personality was done to some extent in TOS and also TNG. If you can accept that, and tone done some of the ridiculousness, then it could work.
"How Sharper Than A Serpent's Tooth" needs to be fleshed out. It's a pointless retlling of a previously done idea, but still workable if you imagine Kulkulkan as a projection in place of what the real alien looks like.
The idea of meeting Robert April in "The Counter-Clock Incident" is interesting, but the whole reverse universe thing is too bizarre to contemplate. The whole idea needs to be rethought.