I think I would largely agree with erinptah. It helps, though, that my main mainstream fandom is Doctor Who, so even when you don't get two women sharing the screen a lot (*bows to your icon*) you can take advantage of the TARDIS as a giant plot generator and introduce your lone companion to someone interesting. Space, time, crossovers (I've written Amy Pond/Kaylee Frye, for example...). And lots of my fandoms do involve that sort of large, sprawling cast and action, so I don't come across that problem much.

Thinking about it, really my only fandoms where the cast is strictly limited to two female characters come in Shakespeare and opera, and where that's the case it usually happens that the pair will have a fairly close bond that you can do something with.