Nope, you are not the only one. I feel the same empathy with the characters. But I did read quite a lot of mangas with one or both characters being bi (can't think of any title right now), although it's true that most of them don't consider that possibility
Well, yaoi was created to aim at female audiences and usually created by female authors, so I think they mostly focus on the cute and romantic yet unrealistic aspect ( ̄へ ̄)
There is a yaoi with a bisexual character though - Hydra. You should really check it out. The story is very original and quite realistic. And the art style is superb.
after reading so many yaoi/BL mangas, i JUST realised, that most of them don't cover the possibility of the seme/uke being bisexual, although, some do. ^_^ Most of the time, the characters always state that they're "not gay/homo" or that they're straight. And then, when they do get into a guyxguy relationship, they think they're automatically gay/homo?!?! just..what?! they seem to skip over the idea that one or both of the characters are bi?! or maybe still straight with that one special exception?!(SP)
it annoys me, because of the denial phases (them not being gay/bi, or them not falling for a hetero guy, not being cheated on, etc) the characters go through during the story/character development, because the characters usually blurt out mean statements. TT^TT Plus, me being me, i always easily feel hurt and annoyed/angry, since throughout reading the manga, i get attached to the characters, and feel empathy towards them. x3
weird, i know, but i'm not the only one right?! T3T haaaaaah~