I've been having a hermaphrodite craving lately (don't read too far into that) and one of my games appears to be coming to an end soon, so I'll have need to replace it! Here's some ideas;
1. A lone male gets transferred into a Hermaphrodite-only school after his old one maxed out. Sexy shinanagins ensue. Can be romantic or just orgies and miscellaneous sex. Idea yanked from somewhere on the internet.
2. Humankind is at war with another space-faring race of (you guessed it) futa. Two pilots shoot each other down over a desert planet. One has lost their legs, the other has become nearly blind. The two enemies must rely on each other in order to live in the desert and send for help. I picture this one as sort of a tragedy
3. A factory farm that produces hermaphrodites and milks them shuts down. One of the 'stock' gets free and wanders into the city. Shenanigans ensue!
I'll have more when I'm not sleepy.
Edit: I am no longer sleepy! New idea!
4. A religious family has two children, a boy and a girl with additional parts. Feeling the girl is a punishment, they give the child away to an orphanage. Many years later the boy finds out and is horrified. He rescues the girl from the orphanage and tires to help her have a normal life, while battling unnatural feelings.