I haven't read too many werewolf stories, but honestly the alpha/omega stuff is the most annoying thing when it comes to werewolf stories for me.
Second most annoying thing is the 'I get more horny / can't control my primal instincts for sex under the full moon' thing (this more a thing for stories where they change at will or outside of the fullmoon)
As for the werewolves gathering around werewolf protagonist, that one I can understand and don't really have a problem with, since wolves are very family / pack orientated. Though I only like this when they're much more like a family instead of... what is the word... ranked/militarized like they tend to be in a lot of fiction.
I also like when it's treated like a curse, is a obstacle in what would otherwise be a normal life. I think 'Being Human' (UK) did that pretty well.