How would you feel if the Aether Foundation provides the player with access to unprecented breeding features that made things far more convenient than ever before, but they do end up being the evil organization, and you taking them down toward the end of the story removes your access to those facilities and leaves you with the usual daycare-couple-on-a-long-route situation?

If the game gave you an option to leave Aether up and running, continuing their nefarious deeds in secret, so you could keep using those facilities, would you? Or rather, what features would they need to have to make you consider it?