"Omega Glory", because I'm just that American
I love the episode because it was grim from the eerie teaser right up to the final, brutal fight. Morgan Woodward's Tracey was a powerful villain in Starfleet clothing, and a great opposite to Kirk.
But my absolute favorite hated-on episode will always be:
"The Empath". So many GREAT character moments in that one; you really felt the love that the Big 3 all had for each other. It also explored the themes of compassion, selflessness, and what a person will do to save the who he/she loves.
I've never understood the hate for this episode; all of your points are spot-on, and one of the few season three episodes to add to everything we know/feel about the big three's bond (along with "The Tholian Web"