I loved the Shepard/Liara romance but it's hard to justify it objectively. It was really Liara who made that romance, considering that Shepard isn't really a character at all. You could see how it changed and affected her character. The devastation after Shepard's death, turning her into a less innocent and more hardened woman. The confusion when he comes back and her desperation in ME3 not to lose him again. She was by far my favourite character in ME.
Assassin's Creed too, between Lucy and Desmond, mostly because it wasn't a true romance at all. You could feel it building up in the first couple of games and it had the hallmarks of something that would blossom into a true storybook romance (without it being directly stated) and then BANG, the ending to Brotherhood comes along and shits all over that out of nowhere.