I suppose there are a couple of ways to approach this kind of "hind sight is 20-20" type thread: you can imagine going back in time to the 1960's and trying to herd Hollywood into doing a better job with TOS by avoid perceived mistakes, OR you could imagine what fan-shows like New Voyages / Phase II and/or Starship Exeter would do to make TOS better today.
In either case, one could argue that, in the 1960's context, the sexism and some of the hokey plot devices (such as a "parallel Earths", probably the worst of them being a tie between "Miri" and "The Omega Glory") are the expected risks you take when you embark on the pioneering new TV show that was ahead of its time. You have to break some eggs to make an omelet, as the saying goes. So, while I agree that the show did make some hilarious blunders, those blunders come with the territory. One of my favorite TOS outings was "Bread and Circuses", a "parallel Earth" ep done right.
But yes, hind-sight being 20-20, women in TREK did get a cringe-worthy raw deal. I'm not sure if introducing a female senior officer to the show (like, maybe, Captain Robin April of the U.S.S. Scimitar) would fly on TV back then, but at least I'm pleased to see Holly Guess' impressive portrayal of Exeter's XO in "The Tressaurian Intersection".
Setting the sexism issue aside, TOS fell into too many cliches. It's like the staff had trouble cultivating fresh ideas. Kirk falls in love. Scotty falls in love. Spock falls in love. Yawn. Another disease, another cure. Another space-monster, another cure. Double yawn. TOS' makers should have learned from their own classics to go back to basics and develop relationships that build the characters and what they stand for. Instead of saying the doomed-other-starship-captain-of-the-week (Decker, Tracey, Merrick), we needed to see Kirk's positive professional relationships with other commanders, working together to deal with situations. I would've loved to see more of Stone, Mendez and Komack, as well as fellow commanders and captains.
TOS showed the Enterprise visiting planetary bases and space stations as ports-of-call, but they did not explore this enough.
I realize that the show had severe budget constraints. but one thing they needed to introduce to expand the TOS worldview was a different class of starship, perhaps a lesser class, that could work with Kirk's ship without eclipsing it. Maybe a ship less than half the size of the Enterprise. Maybe they started to do that in "Charlie X" (the Antares) but the concept was still-born.
I think it would've also been interesting if the show would've shown the Enterprise discovering "lost colonies" on isolated worlds, that being settlements of humans or Vulcans or others that would be descendants of abandoned expeditions. It would be really interesting if these lost communities wound up having some relationship with the Klingons or Romulans. (a whole new dimension to "A Private Little War")
All that having been said, if you wanted to kill multiple birds with one stone, the best and most effective way to do it would be to place Uhura in charge while Kirk and Spock were away. Scott and Sulu hogged too much of the glory. And it would be interesting to see McCoy appointed temporarily by Komack to serve as XO while the Enterprise is sent on a special rescue mission. The role reversal between McCoy and Spock could be both interesting and amusing.