First, please don't write characters so that they automatically touch my Shepard up, playing Femshep with Asari touching my face all the time is creepy...or if you have to code it...then give me an interrupt to slap the hand away.
I don't like romances with subordinates on the ship (official subordinates; in ME1/3 Alliance soldiers and ME2 Cerberus ones), if you are going to do it at least make it a renegade only option...outside the chain of command team mates are ok.
I know that Tali and Garrus fans won't agree, but in ME2 we overhear a conversation where a Quarian and Turian are discussing just how dangerous it is for them to date humans. If you set a precedent like that, then make those romances only open to Renegade Shepard, because Paragon Shepard after hearing that should friendzone the characters for their safety. Maybe even make it so Tali or Garrus turn Paragon Shep down. Try to keep to your own rules.
I agree that not all romances should be straight...but equivalently not all should be bisexual. Have a mix of interesting characters, some straight, some bi and some same sex.
The romance should be recognised midgame not as a quick shag before final mission. Like in DA:O with Alistair, that was pretty well done 
Other crewmates should comment on the relationship.
If the romance runs over several games...remember to write yourselves a note: XXXXX IS A LOVE INTEREST...no more repeats of Thane. You created him for us ladies then you left our romance out to dry in ME3...whilst making forced dialogue flirts with people we dumped/disliked....Kaidan.
I agree it is a bad idea to give the player another love interest that is destined to die no matter your choices. If they want to do it again, well then let the male pc's LI bite the dust. I think the ladies got enough reality in their video game in ME3
. I do not agree with the "get over it" sentiment. I doubt anyone would get over a canon death for their LI so easily. Thane, however, was a warning sign of inevitable death. I expected him to die. His romance was poorly done and the citadel dlc only exasperated the lack of connection with him in Huerta for me. I grappled with how I thought Thane's ME2 writer would handle romanced Thane in ME3. My amateur conclusion is:
1) Thane and Shepard would get a date and love scene that was tasteful (see A Human Day fan comic that his ME2 writer said he enjoyed reading).
2) Thane would try to have shepard and kolyat form a stepmom and stepson bond so he knows his son is safe when he passes and symbolically gifts shepard a son they could never have (I am resentful of the lack of bonding with kolyat in ME3 and in citadel dlc...he seems so distant/possibly angry?? with thanemacing femshep in citadel dlc).
3) Shepard would shed tears at his deathbed and they would say "I love you" to each other one final time (in hospice they tell you to say whatever you need to say to the dying person or regret it forever: "I'm sorry", "I forgive you", "Thank you", "I love you", whatever is needed to be said.
4) I do not believe his ME2 writer would have given him a choice to live
, and I feel that for thane his ending makes karmic sense.
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As for the quarian/turian (fleet/flotilla) convo at eternity, I think someone on the ME writing team was an avid talibration pusher and if they had their way, like jacob, garrus would have been made to cheat on femshep with tali. I honestly see the convo as flawed since a quarian would get much sicker from screwing a turian than a human (transmission of bacterial/viral diseases much easier between two dextros than a dextro and levo...if we stick within ME's lore).
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One other thing. I have noticed garrusmancers and thanemancers at each other's throats sometimes. All the femsheps need solidarity. Now from a purely psychological/emotional point of view I ship Shakarian; the two hardcore soldiers who are out to dispense justice in an unjust galaxy (reminds me of Drake and Vasquez in Aliens), and have leaned on each other's shoulders since ME1. Thane's limited lifespan along with the whole dead wife thing really hampered the development of their relationship in that limited time they had (please ME:Next writing team do not combine carth syndrome and impending death in the future...a toxic mix). I am regretful I had to mod the game to romance Thane with my maleshep, but had thane been a bi option, I could get over the dead wife thing by reasoning he was gay and in the closet during his marriage
.