I didn't like the self-cleaning.
(How long do spoilers last with these things?)
This could have been an ongoing arc that crept up from time to time about emancipation, civil war and reconstruction.
Unless the Klingons or the Romulans took the Orions side, how long would they really last in an all out war against the Federation?
The Orions still use atomic fission to power their warp drives.
What exactly would the Federation do if they had conquered Orion?
And how would that lead to the humanacentric Orion Syndicate as seen in DS9?
What if Kirk had gone through with rescuing the slavegirl before he couldn't?
Imagine Commodore Gray decking him with one punch... "This is what happens to assholes who do not follow my orders!"
Meanwhile having a drug that inoculated the crew was nice, but what if the only way out was to still have one of those marriage sex melds Trip and T'pol had that everyone on Enterprise in the Eyes of Vulcan legality was massive married big love clot of polygamy?
Remember the Telepath rail road from Babylon 5? It was a year later since the station first dealt with the problem of runaway telepaths and Sheridan is looking for the area leader of the illegal underground on Babylon 5, and it turns out to be Doctor Franklin, another main cast member who had been morally swayed a year before to get up off his as and do the right thing no matter the consequences.
I understand that the writers can't over complicate things, and keeping with the patterns of the original show that they have to tie everything off, but how much difference would it have made if Kirk had challenged Lou Ferrengo to a bowling competition match, while Lolani boosted his ride, so that she could run off and start a grass roots movement to free her gender?