Plato's Stepchildren is an episode I have mixed feelings about. I do agree there are some great character moments. The scene when Kirk/Spock/McCoy are talking about controlling their hatred with Alexander I think is one of the best moments of the Star Trek series.
I also think Alexander is one of the best guest characters.
However I think the series went way too far with the torture scenes here. Unlike a lot of people I don't find anything amusing about them, I find them deeply horrible (which I think is the point) but I still think the show made a mistake to have two long scenes like this. Especially some things in the 2nd scene are really bad writing choices for me: having Spock sing, everyone dress in togas. I think it actually took away from the message they were trying to get across by going overboard.
Also the kiss scene between Uhura and Kirk might have been progressive for the time but considering they were forced (and Chapel and Spock) the scene is just so unpleasant to watch. It doesn't send a positive message of equality at all.
I think if they focused more on the psychological side of what this did to Kirk/Spock/McCoy and less on the physical torture this could have been a better episode.