Yeah, the only time that Trek really introduced a science fiction idea in order to explore it was Star Trek: The Motion Picture.
It wasn't much of an idea. Certainly not by science fiction standards of the time, anyway.
"Doomsday Machine" and "The Ultimate Computer" are not about the dangers of automation.* "City On The Edge Of Forever" is not about the ramifications to causality of time travel. "A Taste of Armageddon" is about civil disobedience, not computer war.
Star Trek used sf conceits often to explore other kinds of ideas. "The Enemy WIthin" is, if anything, a rumination on certain aspects of human nature. That's not a science fiction idea, but a philosophical/moral/psychological one.
So what's up with all the "Where are the new civilizations and new worlds" stuff, anyway?
Bruce Sterling once gave an address in which he said that the one thing science fiction really did that no other popular genre did was to evoke a sense of the weirdness of existence. His advice to a group of game designers was this: "Follow your weird."
"Children of The Comet" and "Charades" both had more than the Trek-standard dose of strange new aliens. Only once or twice in TOS were aliens that were very weird and different anything more than catalysts to motivate human characters and their adversaries in outlandish costumes into more prosaic conflicts.
I think some fans are just hungry for more weird. Maybe when Trek was new the very nature of the genre - look, people in a spaceship, and aliens! - was sufficient to provide that, given that the storylines almost never did. But we're all way past used to that, now, and think that Star Trek has lost something when really, we have.
*More than anything else, they're both character melodramas. Decker and Daystrom are men tormented by responsibility for their mistakes, each in his own way.