Yeah, in reality, Homura Akemi is just the best character*, regardless of presence in anime, gender, sex, or whatever. Otherwise, the best feminine anime character I can immediately think of is probably Yui Ikari, the best masculine anime character I can think of is Kaworu Nagisa, and the best androgynous one is Kyubey.
I am letting my biases show.
Other great anime characters:
Kyon, Haruhi Suzumiya, Sakaki, Osaka, Faye Valentine, the trucker from Cowboy Bebop whose name escapes me, the blind woman from Cowboy Bebop, the creepy clown assassin thing from Cowboy Bebop, most characters from Cowboy Bebop.
*With the possible exception of the bowl of petunias from The Hitchhiker's Guide To The Galaxy.