Imean, Voyager had half the crew be secessionists from the Federation who attempted mutiny on at least one occasion and had massive behavioral problems. They got resolved, but given that we're all of two episodes into LD and it's getting blasted for that, I hardly think those complaints are terribly fair.
I do agree with you on the failings of parody and comedy.
That wasn't a great example you linked, since Bones was proven correct in, like, the very next scene. And, more to the point, he was generally portrayed as being correct, to the point that many of his jabs closing out the episode and pointedly noting that the pure human ways were how they solved the plot of the week (Spock's rejoinders tended to be more for comedic effect, even if they did have points).
ETA: I do feel a bit bad here as I have you at a definite disadvantage; TOS is my favorite. Hell, just now I decided to put it on as background noise while I do other stuff, because why not?