May I suggest upgrades to the huts to expand the capacity? It's particularly needed for ones with multiple species. Plus we probably need some kind of money sink after they are all built. Maybe other features could be available like automatic milkers (reduced amounts but consistent), expensive aphrodisiac flowers to give a boost to lust, something to passively increase xp a little each day, and other things along those lines. Maybe some upgrades could also be available to the breeder's house as well.
Another idea I had was for the Breeder to somehow be granted certain traits from the named Nephelym (Town NPCs and the keystone NPCs), maybe through more advanced breeding requests after all of the gates have been opened. For example, you would be able to get the Nymphomaniac trait from Cassie, the Slim trait from Monarch, the Fertile trait from Autumn (Dryad), the Stoic trait from Emissary, the Potent trait from Fern after her final form, the Kindhearted trait from the Reaper (plot twist), etc.
Going off of that, there could be the potential to level each trait by completing even more complicated breeding requests or performing some other task.