For an episode that piled up the inconsistencies to the point of absolute breakdown, my vote would be "The Alternative Factor." Voyager's "Threshold" and its ultimately inconsequential Warp-10 nonsense is a close runner-up.
Same here.
Crap, how many minutes did I just spend writing about "Threshold?"
Your post sums up the problem pretty well though.

Did the Doctor say how lucky Tom and Janeway were to have been desalamanderized? I forget...
You know, I could buy it, if Janeway wasn't willing to return to the Alpha Quadrant by that method, if she (and we) knew that roughly one-third of the crew wouldn't survive the desalamanderization process.
There are plenty of rationalizations to try to make this episode work. I won't offer any more, but I do have a new perspective. Anyone notice how the concept of the 24th-century "evolved humanity" was taking a beating on DS9 around the same time? "In the Cards" from a year later, for example.
Here's why. The characters stopped extolling the virtues of "evolved humanity" once "Threshold" showed what they were evolving into.



TOS: The Enemy Within...Sulu and his guys are stranded on a freezing cold planet because the transporter is broken. No one thinks to send a shuttlecraft to pick them up.
I know that the "real world" reason for not using a shuttlecraft in the story was because the models and/or sets weren't built yet, but I believe that the concept of the ship having a set of shuttlecraft predates the filming of this episode, as the shuttle bay doors were part of the ship's design from the beginning.
According to Memory Alpha and the Star Trek Encyclopedia, the existence of shuttlecraft or a hangar deck had not been established even among the writers at the time the episode was written. At the time, writers were under the impression the transporter was the Enterprise's only method transportation on or off the ship.
That's still irreconcilable from a meta perspective, then. The writers assumed that the only access was through a fallible high-tech device??? Forget this episode — what was the crew supposed to do if they had to abandon ship in a hurry?


