To be honest, the Geass show surprised me. I know other anime adaptations have previously cut the female characters out completely (this is what they do for the Prince of Tennis shows, for instance) but I can't think of anything that's cast men as female characters before.
I think there's a couple of reasons why all-female casts are popular, particularly with shows based on anime:
i) For something like Sailor Moon or Utena, where the target audience is pre-teen to early-teen girls, they don't care about boys in the same way.
ii) The Takarazuka (who do many of these adaptations - they did the Phoenix Wright show in 2009, and have previously done Black Jack and Rose of Versailles) are all about heightened fantasy and emotion - like shoujo manga, really. Reality is discarded entirely and the lush sets and over-the-top performances heighten the overall experience. The actresses are trained specifically for "male" and "female" roles and there's a big female fandom surrounding them as people and performers. I think all of this contributes to something which is much more popular with women than with men - and it just so happens that they are the ones doing stage adaptations of melodramatic anime/manga/games!
So I guess it's partly about what the audience is looking for and partly where the talent actually lies (and who's willing to stage these shows).
Of course there are anime adaptations with mixed gender casts - Bleach and Ao no Exorcist, for instance. But many of them go with all-female casts purely because they're done by the Takarazuka!
(this is OT, but the Takarazuka are owned by TOHO, who also have their own "normal" theatre production arm that stages shows with mixed gender casts. The companies have been known to stage the same shows as each other in radically different versions because the Takarazuka's audience are looking for a "hyper-real" experience - they cut plays and musicals to remove all political storylines etc. because they have no place in the "world" of the Takarazuka.)
