My intent is not to allow genetic augmentation to give a character Learned qualities, but Innate qualities. The character creation Build Point limits for these qualities is for balance, true, which is why they would cost Essence if obtained through augmentation, so as to maintain that balance.
A quick list of qualities that would normally be character generation only, but available through genetics are as follows (there are a few more available through genetics or cosmetics, but not *normal* advancement):
- Natural Hardening
- Photographic Memory
- Natural Immunity (already reflected with Genetic Immunization)
- Quick Healer
- Biocompatability
- Type O System
Now, if we, for example, decided that the cost for such a treatment would be (BP Cost / 5) x 0.1 Essence & (BP Cost) x 5,000 Nuyen, this may be doable while still maintaining game balance. Sure, being able to take Type O System after character creation is powerful, but is it really worth using up 0.6 Essence for a reduced cost on your bioware? For some characters, yes, and they would shell out the 150,000 for it. For others, not really.
Also, I already said that, for reasons presented in the Augmentation fluff, Awakened qualities & Technomancer should not be available this way. And I never mentioned using it to increase attributes, special or otherwise. Those are to be increased with Karma normally, and are not a genetic feature anyways - maximum potential for Physical & Mental attributes is, but not their actual level.
Note there are also a few negative qualities that normally could not be removed, but would be able to with genetics, such as Sensitive System - for the negative qualities, I would rule a fixed 0.1 Essence cost, but you also must pay Karma as normal to buy off the quality.