Why do most of the best anime have female main characters? Examples include: GITS, Lain, Angel's Egg, most Ghibli, Utena, Satoshi Kon movies, most WMT shows, Tutu, Doremi, Haibane, Windy Tales, Precure, Sailor Moon, K-On, Tamako Love Story, Erin, Azumanga, Nichijou, Kare kano, Rose of Versailles, Aria, Belladonna, Dennou Coil, Kino, Euphonium, Moribito, Birdy Decode, Twelve Kingdoms, the list goes on.
I think this is the only medium for this to be the case.
Because the anime industry has no issue writing them however they please instead of worrying about getting their throats torn out by the media for being sexist. The worst thing they have to sorry about is stepping on some otaku feet or pissing off irrelevant foreigners but it isn't that big a deal comparatively
I am literally going to marry Azusa.
I also wondered about thia. I like all the shows you mentioned and even some shows without female protagonists I like: Eva, FLCL, Kaiba, Tatami Galaxy, Texhnolyze and Beautiful Dreamer all still have interesting and important female characters in the main cast. Only examples I can think of without those would be Mushishi and Mononoke, but both of those don't really have much of a cast in general.
I think the reason is simply because there are a lot more female characters in anime and manga in general. Maybe it's because most of the creators are men so they prefer creating female characters. It might be also because they know it's men that mainly watch anime.