Just thought of one nice one. When levelling up, give Learning Points. Could be some sizable chunk and would basically offset the fact if you capture a higher level+grade they'll just come with the higher stats. Something like (100 + level * 5). You're then free to assign them to skills or stats. Wouldn't really be game breaking, but once you're gaining those early levels easily, you can get a bunch of skill points to either get skills or boost stats. Still be faster to capture higher level, but at least if you instead level up you're saved effort of training everything.
How about a mod that greatly increases rebelliousness based on level. Then makes it so amnesia potion has a chance to fail based on that (now high) rebellious streak.
Those powerful high level bandits and monsters you catch are gonna take extra work to tame. So training up a more malleable low level slave seems much more appealing.