I first encountered ENT in reruns, so I was behind the times. That having been said...
"In a Mirror, Darkly" was the umpteenth attempt by the Berman sub-franchise to capitalize on the "alternative universe"/"alternate reality" trope, and, looking at these stories strictly on their plausibility, I would say that the only one of these that holds up is "Yesterday's Enterprise". None of the others ever made any sense. It's all "let's try tinkering with the sets and costumes and get all the characters to act like Nazis, for a neat-o story idea" gimmick.
I'm going to disagree with your characterization of IaMD as the same type of alternate universe story that YE was.
YE was an alternate timeline
set in the real universe involving real universe characters, in other words, the characters we had known from the beginning of TNG.
IaMD is an alternate universe
set in a universe which is not the real Ent universe and involving alternate
characters who were not the characters we had known from the beginning of Ent. Thus there is little emotional investment in these alternate Ent episodes. The emotional investment in the YE characters had already been established because they are the [i]real[/] TNG characters.
YE had the easier task of seeming more meaningful and "important" because it involved the regular TNG characters but in a different timeline. Had we gotten to know the alternate IaMD characters better (which was the original plan) we may have had a much more satisfying experience with them. Mirror Mirror was no less disposable.
My point is that it was easier to create a more serious and impactful episode in YE because it used the regular TNG characters with their reality altered into an artificially created different timeline.
If you'd like an example of the level of profundity that could have been reached given time, read the compilation, Glass Empires.