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I need one last piece of advice, really. The balance between patience and discipline is hard to find. Ignore their reluctance, and they get worse. Beat them too much, and they get worse. I've tried mixing up the sexual and non-sexual requests, but that also seems random.

What is the best way to raise their acceptance? In one playthrough, I've had all three girls fully trained in all aspects, yet their other stats never rise. Doesn't affection for the MC ever develop?

Each girl will have three loyalty quests, more or less.  Their willingness to be obedient increases with the first, and affection begins with the second.  It sounds like you're mostly at the end of the existing content.  Moree to come soonish.