While the Crafting system is not as up-to-date as some would like it to be, maybe one way to infuse life back into it would be to make it possible to "Blank" augments to craft abilities.
Obviously leave the Color code and what kind of crafting can be accomplished on them as they are - Preventing Weapon Effects on Colorless Augments etc. exception being at the Flexible Crafting Range
The Starting Crafting potential can be limited based ML of the original augment. Should only work on common augments and not able to be done on Named Augments.
This would open up additional gearing options as well.
Special rules may need to be employed for Gear that is crafted upon that also has augments slots, but I think ML restrictions may be able to resolve this, because at worst this would allow 1 extra Prefix/Suffix for each Augment slot allowed on gear. But this might make Crafted Gear more popular pulling people back into that part of the game.