There were more good moments in Season 3 than bad. Heck, even half of Spocks Brain isn't a bad episode, even though fans have made it notorious. There were also some bad episodes in the previous seasons, like The Alternative Factor or The Omega Glory.
"Alternative" should grab me more, but the whole thing tries to emphasize EPIC DISASTER, FOR THE ENTIRE GALAXXXXYYYYYYY!, and just falls flat. Maybe the technobabble used in 1966 made it easier to buy into, but (IMHO) it doesn't hold up for that alone...
"Omega" started out with a very interesting sci-fi/horror premise and, of course, evil Cap'n of the week with Ron Tracey (Morgan Woodward being one hell of an underrated actor). It's only when the "it's another parallel to Earth development, and so closely so that the inhabitants wrote in full English, had some consonant drift and altered meanings as expected, and nobody on screen is sure if they're supposed to be surprised or not because this is like the 8th planet by now that's just like Earth save for the immortality thing that at least had a good reason for it being that way" scene occurs that starts to drag things down. At least for Star Trek.
TOS's "parallel Earth development" stories aren't bad, apart from not fitting in TOS's mission/vision statement of boldly going where no one has gone before. fit more at home in other sci-fi like "Sliders", a show where it's exploring multiple Earth development scenarios based on a theory proven right by some nerd-who-looks-like-footballplayerstud by sheer accident but at least his professor is duly impressed. That is "Sliders"'s bread and butter, not exploring the whole of the cosmos looking for strange new worlds and civilizations, mostly because they'd be and act far differently to situations on Earth... TOS used the notion as a budget-saving trope, and the fact that so many of them are still watchable if you roll with the traipsing outside the show's premise and with such flagrant absurdity is also impressive. But if I was watching the show on autoplay rather than looking up story titles to click on, every time a "Yo Jim, it's yet another parallel development" reveal where half the time they're shocked when they shouldn't be or vice-versa, I'd still roll my eyes and then "Oh yeah, I remember this one, it had x and y moments or at least enough eye candy with her and/or him to be distracted by, whee!"