Yeah, half of the reason I stopped reading SGVY was after Yuuki started developing apparant romantic feelings for a male classmate - transgender fun is alright in itself, but you don't see Ranma hitting on Ryouga or Kuno or Happosai, do you? If SGVY's authoress decides to ditch the Yuuki/dude pairing and go back to the Yuuki/chickwhosnameIforget pairing that things seemed to be building up towards at first, I might start reading it again.
Back to the transgender Shinji idea, Shinji's attempt to explain his predicament alone would be worth a oneshot. Gendo: "Correct me if I'm wrong... but didn't I have a son?" Shinji: "That's a funny story... erm, you see... have you ever heard of Loki?"
Which for some reason brings about another idea: NGE/The Mask crossover. Yes, Mask Keitaro is all good and fun (and when's that fic coming out anyway?), but just imagine wtf would happen if Shinji were to put the Mask on while, say, piloting an Eva?