I think it is best to have different augments that do different things. It really changes up the gameplay each time that way, depending on what you get. I really like that all of CE's augments are so unique and useful in their own way. There really isn't much that is a "must have" so you can just try out different playstyles. The only reason I thought the trade goods should not be augs is because of how many new cool augments CE has and it is nice to try out all the new cool things, even on a trade ship loadout, but I understand your position.
The possibility of upgrading certain augs is very cool though. You can't really increase the Mantis Pheromone ones or the Engi ones in the way proposed above, but I like that you can stack the Rock and Crystal augs now and that you can Engineer improved scanners for the Stealth Cruiser. If upgrading augs through engineering could be expanded any further I would be all for that. Also, because I like that upgrading the faction specific augs gives you an even bigger practical incentive to keep each of them and makes each faction ship more unique.
Anyone else have more ideas for engineering?

I really like that system!!
--I thought about maybe being able to engineer a Mapping Computer if you have maybe Drone Control and/or a certain type of Drone or maybe Drone Control and Long-Range Scanners.
--Or being able to engineer a hull repair drone if you have a Hull Repair Kit/Arm.
--Or maybe even being able to Engineer Long-Range scanners from lvl 3 sensors
--Having engineering options with more than 1 requirement would be cool
--Being able to upgrade certain weapon and drone types to the next "tier" would be cool, but for a very large amount of scrap to make it not normally practical unless you desperately need more firepower. Or maybe even being able to construct a very basic tier weapon of some type depending on what augs, weapons, or crew you have currently.
--(Maybe there could even be an augment that allows you to make engineering improvements more affordable, or opens up other special engineering possibilities?)
I don't know just brainstorming here...