No, I agree with you. As I said, I don't like it that they are forced into the same roles, but since it's part of their character development in the game, there's nothing else left for me to do than accept it and make the most of it. It's still part of those characters now. They've already been written.
I must disagree here. Mars and the Citadel Coup do take romance into account. Even if the most visible difference is the change in dialogue and some animations. (FemShep can actually act fairly touchy feely on Mars if Kaidan was her LI and Kaidan doesn't shut up about how much he liked/likes her but he's still trying to wrap his head around what was her relationship with Cerberus. That's all there is to it. He wants to make some sense of it.) I actually feel that they act fairly unprofessional on Mars because they chat about their relationship almost more than about the mission if you go the "paragon" route. (Not that I don't enjoy the drama.)
During the Citadel Coup, you even get additional points for having romanced the VS and staying faithful to them/admitting you've been with somebody else. On the outside, that means they trust you more than if not romanced.
Since I do romance Kaidan, I spent some time thinking about where Horizon puts them. And I came to the conclusion that the VS's mistrust is perfectly understandable. As I have said in my long-ass post before, there's no reason they should trust Shepard. Given the circumstances, Shepard is either a traitor or a clone. Take your pick. (My Shepard had a scar on her face in ME1 that completely disappears and instead has glowing scars in different places in ME2. That wouldn't freak anybody out.) The fact the first thing the VS does is that they hug Shepard when in romance, before it hits them how goddamn surreal this situation is, is freaking dangerous as hell to begin with. Shepard was gone for two years - no messages, no nothing, then shows up with terrorists. They would be stupid to trust them. That just makes me think that my LI uses their brain and not their emotions because, "OMG WE SLEPT TOGETHER TWO YEARS AGO," is, imo, not good enough justification to trust somebody when your dead lover magically returns without letting you know and working with the enemy. Did they act emotional? Sure. But their reaction makes sense and they soon apologise for it.
To me, it's Garrus who acts weird. He has no reaction at all. He's like, "So, you're back, okay, lol." Then he gets freaking shot in the face and fixed by Cerberus so he doesn't really have much choice in the matter. He pretty much owes Shepard and Cerberus one. Tali doesn't follow you until much later, until after Horizon, and she might not follow you unless you track her down and save her ass... yet again.
The VS later at least apologises for their emotional outburst and confesses how they felt about it all, even if it's just a goddamn mail, and ultimately it's Shepard who cannot answer their message and you're not allowed to meet them again until ME3 because the writers wanted to get rid of them for the rest of the game. (I totally expected some Citadel meet-up with them later in ME2.) Then I freaking blow up an entire star system with my Mindoir Shep which makes her look like a real terrorist (and there's no other witness besides Shepard)... yeah, that's not awkward.
So, yeah, if after two years of believing somebody was dead, you'd be able to trust them the second they returned with Cerberus backing them up fully and without a question, then I applaud to you, because I probably wouldn't. And even if my Shepard didn't have a full understanding of it, it's not like you can suddenly turn your feelings off and move on to another person like nothing that happened between you mattered.
And that's not to say that moving on would be wrong. Not at all. That's just how I see it. If I dramatically end a relationship, starting another one would be pretty low on my to-do list.
The hospital scenes actually give a lot of closure to the romanced relationship and send it the right way. It also contributes to the outcome of the Citadel Coup.