After reading a lot of the responses here, I'm finding myself drawn to this episode even more. To watch it again with a critical eye on Jellico.
So yes... despite the "set up" for us to hate Jellico because he effectively replaces Picard and to feel for Riker because he misses his captain, the unlikable Jellico is really a man who is faced with a very difficult situation and must make the most of it. No honeymoon with the crew. He has to "get the job done" with everything else a lesser priority.
When Deanna was gently trying to play nice with Jellico and tell him sweetly how the crew would only love him if he showed some warmth, it was... well, rather like a "reset" in perspective. How unprofessional she looked in saying this. And then for Jellico to knock her back in line with the bit about wearing a uniform. It was like "it's about time!"
Actually Deanna could really be one of those officers who wears a shawl or some other covering during her sessions to help tone down the "military look" of the uniform, then leave it behind when heading off for other duties. In any case, it was a nice evolution of her character to eventually dispense with the civilian clothes in the latter half of the series.
Anyway, with a little more careful attention to what transpires in this episode, it becomes clear of just how marvelous a performance Ronny Cox gives. He has had the habit of taking up a lot of unlikable roles in the latter part of his career, with a lot of sometimes forgettable minor characters, but the man does have talent. I hope he gets an opportunity to do some greater shining before he gets too old, much the way Jeff Bridges had his career revival late in his game.