Have you seen .hack//sign? There's both femslash and female focused aspects to that show (which is sort of spoiler, so hopefully that's vague enough if you haven't seen it, it's not all obvious on the surface but I'd argue that's all pretty cannon).

Also can't believe I didn't originally think of:
- Puella Magi Madoka Magica is definitely female centric, and so much femslash potential/shippy-ness. It's also super dark, with major twists and makes many people cry so forewarning. It's also got a decent sized fandom I think?
- Tamora Pierce has some fic for her work, but cannons are all awesome female-centric stories! :D
- Tokyo 8.0 is one of my fav. animes of late. It's super good, geologically accurate, and the last ~3 eps had me bawling like a baby so warning for tragedy, but it's got 2 amazing central female characters, one's the main character, another is a well developed central-focus supporting character.
- Orphan Black, if you haven't seen it, it's really good, lots of female characters, 1 set of whom are in a romantic relationship with each other. Haven't looked into the fandom beyond vids tho.
- if you're looking for RPF, there's TSwift/Karlie Kloss, or KStew/Charlize.