The one main thing that bothers me when it comes to a lot of yaoi is this extremely stubborn attitude about top vs bottom (or rather, gender roles shoved into gay relationships).
While it is true that some people prefer to be top or bottom entirely, it would be entirely untrue to assume that all do or that it's even the general trend. Having a couple that goes into these roles naturally by their own preference is fine in my mind, but the whole ordeal where the more masculine one basically forces the smaller person to be bottom is overdone, boring, unrealistic and unhealthy. At least most of the time I see it done.
Don't get me wrong, having stories where this happens would be fine since almost anything is fine in fiction, if it weren't for that it's so common that it's messing with people's understanding of gay relationships (and any other relationship as well).
I tend to write vers couples and I cannot even begin to count all the times I've had confused young readers shouting about "WAIT WHO IS THE BOTTOM I DON'T GET IT?!?! EARLIER HE TOPPED BUT NOW IT'S OPPOSITE I DON'T UNDERSTAND SOMEONE HELP" in the comments.
This isn't even only hurtful to gay people. It's not a gay issue. It's a sexism issue. Because of this perceived "must-be" dynamic, tons of straight men don't dare to let their partners take lead in the bedroom,and let's not even mention playing with the prostate, out of fear of being seen as gay or weak. On the other hand, tons of straight women have their sexuality emotionally restricted. It affects lesbians too, lesbians keep being asked who's "the man in the relationship". It's just bad for everyone.