I've just read Nana to Kaoru and really loved it. The female didn't seem so weak and the male wasn't so overpowering in my opinion, I really liked how they were portrayed as characters! But there were a few chapters that involved the male getting dominated. I wanted to know if anyone knows a good femdom manga with actual plot and a long story. Also with no meaningless sex. :/
Not sure how graphic you want the content to be. Here are a few suggestions anyway :
Aku no Hana. More about psychological domination than physical domination (almost no erotic/sexual intercourse) Sundome. I hated it but from what i remember it seems to fit your description, more or less. M.
I'm also interested in what you or others would recommend in this department, provided, as you said, it's got actual plot and characters.
EDIT: and though the female protagonists have roles of their own, the main characters in the above list remain male (are you only after female MCs ?)
Ahaha I've read both already and loved them a lot! Nozoki Ana was a good one with a controlling fem lead. The MC was male and the plot was a little lacking. The author kept adding more girls once the previous one left. I enjoyed it nonetheless. It was also pretty long which I liked. I don't really mind how graphic or not it is either.