Milady wrote an interesting post on the evolution of Bioware's romances on her site Hypercritism. I started to post a response, but then had to think about it some more. It seems to me that the real issue is not so much the writing of romances, so much as it is the underlying companion affection system.
The companion affection system reminds me of valor points in WoW. The connection is probably not obvious, but they're both systems which have been iterated on over time, and which may no longer serve their original purpose.
Think about why Bioware came up with companion affection. What problem was it intended to solve?
In the early Bioware/Black Isle games, your relationship with a companion was really independent of your actions in the game, independent of your character's nature. Really the only thing that mattered was your previous conversations with the character and your progress in the game. Those were the keys which unlocked subsequent conversations.
I think the original idea behind companion affection was that your character's personality--as revealed through her actions in the game--should matter to your companions. A good-aligned character should find it easier to get along with other good-aligned people, and harder with people who share different values. I think this idea makes sense, and is a reasonable behavior to try and simulate.
So Bioware decided on a simple scale. If your character took an action or dialogue a party member agrees with, your affection with that character increases. If they disagree, the affection decreases.
The next hurdle comes when you have more companions that party slots, and the game has roles. If your character fulfills the same combat role as Alistair, you're not going to have him in your party. But that means that Alistair's affection does not change, and so you will never see Alistair's personal storyline.
So Bioware implemented gifts. Gifts allow you to increase the affection of companions you don't adventure with. In The Old Republic, gifts also allow you to increase affection if you don't quest, if you PvP or do space battles or group instances.
But if you think about it, gifts also invalidate the very purpose of the companion system. Your character's personality doesn't matter to the companion any more. Instead you just ply them with gifts until their stories unlock.
What the gifts do is turn the companion affection system from a simulation into a grind. Another xp/rep grind that you fill out for rewards or to unlock content. I bet many players in SWTOR will have all five companions with their affection maxed out.
The other part of this is that players, especially MMO players, don't really like making permanent decisions, especially decisions that close off content. Gifts allow you to circumvent the choices made during leveling. Your choices are no longer permanent.
I think that companion affection systems would work better with two changes. First, no gifts, no ways to circumvent the choices you make in the game. Your companions react to your character as revealed by the choices you make.
Second, changes in companion affection are not restricted to your current companions, but rather occur for all the companions. This means that you can't avoid the loss of affection by using a different conversation. Conversation and decisions trigger a reaction in all characters, so a decision might see a gain in affection for some characters, and a loss for others.
Of course, the downside of this is that you won't see the stories for all the companions. Maybe the companion affection system is entirely unnecessary, and the old way of unlocking stories as the game progresses was just better. Maybe trying to make your character's personality--outside conversations with companions--matter to your companions is not worth the effort, and has too many negative consequences.