Somewhat related to the very emotional men is the guy who's supposed to be tough, but is having an emotional breakdown, and is often full of self-pity. This apparently comes from fan fiction, and probably ties into the stories in which a character is put through a hurt/comfort scenario. I don't personally care for reading about an emotional wreck of a character -- how realistic is it that he can have a healthy relationship if he's in that kind of state? I want for both heroes to have their strengths, and to work well together, not having one constantly rescuing the other.
Which leads to the alpha/omega thing. Bigger guy is dominant and doesn't have any faults except for bossiness, smaller guy is weak and submissive. Boring. I know that scenario works for some people. It just doesn't work that well for me. In my post about queeniness, I talked about at least mixing up your stereotypes. Why have characters that are just cardboard stereotypes? I want to read about characters with depth and complexity.
I don't know if I've seen this pet peeve mentioned before: too much barebacking. If you've established that the couple have been tested and are monogamous, that's one thing. But too often, you just have the characters telling each other that they're clean, or not asking at all. I think this is part of why vampire and werewolf characters are so popular, as the mythology generally is that they don't get or transmit human diseases. But if it's a non-paranormal contemporary, the characters should really be using protection. I suppose that this is from hanging out with my gay friends in college in the early- to mid-nineties, when AIDS had decimated a couple of generations of gay men. My friends were very aware that they should have safe sex, and talked about how to negotiate it. Contemporary m/f erotic romances have the hero using condoms. This should be the case for the heroes in m/m romances as well.