I was thinking about this for a while and then I read this post Augmentations just reskinned mutations... MUTATIONS! which echoes some of my thoughts on the matter.
In short, IMO the way soldiers are currently augmented is a missed opportunity, narratively speaking. Perhaps the current system is just a placeholder and something like what I will suggest is already being considered by the devs.
What I think is missing is some art and a short text vignette, at least for the first mutation and the first bionic operation. Phoenix Point has some very cool art and it would be great if something like, e.g. the pictures for the trade screen (I’m a big fan of those - does anybody else think that they really add a lot to the narrative and to the atmosphere of the game?), could be used to depict the aug operations.
The other thing is that the instant augmentation feels wrong. This is one of those cases where making players do things and have them wait would be a good thing, IMO. That is, have them transport the soldiers to a base with the requisite facilities and wait a few days. It adds some much needed drama.