Traynor is definitely a subordinate relationship. Everyone on the ship is, honestly, even if they tried to play coy with 'the regulations don't technically apply.' Shepard's still the boss of the team and the ship.
About the only non-subordinate sex scene Shepard could have in the entire trilogy was the Consort, and calling a relationship is, eh-
Considering how much time Shepard spent on the Citadel and Omega, it wouldn't have been hard to have a lover at port for when you returned.
Actually Kaidan being a Spectre puts him on the same level. And in the Alliance, with Shep's demotion and Alenko's promotion, I think he technically outanks Shepard in that regard. Ashley's rank is about equivalent to the Commanders' in the third game, I think. Even if Shep is in charge, the VS romance option, by the third game at least, is on more or less equal footing with Shep. I view Garrus in a similar light because he's risen in the ranks within the Turian Hierarchy. (Generals are saluting him, remember?)
I was actually not surprised when Thane died. I mean, you go into that relationship knowing his illness is terminal. Might as well give him the chance for a heroic sacrifice. Even with their future science, a feasible cure for his syndrome is years away. It's not like he and Shep were ever going to have a traditional 'happy ever after' romance. I actually liked the Citadel additions for Thane too, because in the vanilla game it seems a bit weird that Shep doesn't seem broken up about it ever.