I would have loved to see You Only Move Twice extrapolated into a feature film. Supposedly Albert Brooks did so much great improv as Hank Scorpio during the recording, they could have cut around 3 or 4 completely unique episodes of his dialogue. As awesome an episode as it already is, I imagine they left so much on the table, so much 'dysfunctional Springfield' business in the first act, fleshing out cypress creek as a town, bart and lisa in a new school etc.
On the commentary for 22 short films, they also mention floating the idea of a spin-off show called Springfield, where the Simpson family are basically not involved at all. that's another feature length idea I think they could have really hit out of the park, although I understand there's no chance it would actually have been greenlit