I always saw that scene as problematic. I'm fine with Troi being in the standard uniform (and think it might have been better to put her in one from the start, or at least have her in the skant with a pair of black leggings and normal shoes) I'm even fine with Jellico ordering her like that to drive the point home that he's an harda**. But I'm not alright with the idea that a permanent change to the character happened because someone ordered her. I'd rather have the permanent change would have happened as a result of her promotion in "Thine Own Self" because SHE chose to make the change. As it is it looks like she was bullied into it. It doesn't help that every universe in Parallels in which Picard died in "Best of Both Worlds" (and, in turn, in which Jellico never became Captain of the Enterprise) still shows her in her turquoise dress on the bridge, even if the universe was overall more militaristic, further implying the permanent change only happened because she was ordered. So basic clay I would have preferred: Uniform under Jellico -> back to causal attire under Picard -> Back into the uniform starting with Thine Own Self.