Here are some Ideas floating around in my Head:

+Probably a new Slot (Spine or something?):
Probably by the use ofthe Dragons Breath add something to fly, like wings etc..
That would make that augment late game, since you need to have beaten(or at least have met) the ender dragon.

+For the Eyes Slot:
I don't know if this is possible, add the feature to implant existing Overlay-Adding-Things into yourself (I'd be interested in seeing something like that for the mod OpenGlasses. That'd be cool ^^)

+For the Feet Slot:
Something like Flipper-feet to be faster in water

Spine slot:
I'll consider it if I can come up with some interesting upgrades. Not sure how I feel about flying since there's the Vanilla Elytra and jetpacks from other mods - but I'll think about it. Something like jetboot Cyberlegs is the most theme-friendly thing I can think of.

Eyes Slot Overlays:
I'll look into it. Could you link me to some existing mods that have overlays? This could be things like what you linked or things like the Goggles of Revealing from Thaumcraft.

Flipper Feet:
Already implemented to some extent in the dev branch, but I'll probably tweak them and add a Cyberleg-less alternative.

Good question, when I first thought of that Idea, I thought there were more. I'll gather some.

Possibilities:

1. The One Probe The API Can be found HERE
2. The Sonar googles (Can't really remember the mod it was from. Probably Extra Utils)

Can't think of more currently, when I find more, I'll add it to the list :/

Edit:

The Spectral Glasses from EvilCraft seem to add some sort of functionality. I havent played with the mod yet so I don't really know their function, but here is a picture of their description:

I'm a picture! Click Me!

I didn't want to open a new issue for this so I'll just add to the ideas. I'm sure it's been suggested before, but an augment that has a small chance to keep your augments on death would be nice. Stacking them would to increase the chance would be pretty cool, but obviously there's always gotta be that possibility that you lose augments.

I like the idea of keeping augments, but there's two problems to that. A) You respawn with no power, thus with some augments you can't even move. B) You die from no essence and end up in an infinite loop.

My suggestion would be that all powered augments are lost on death, but you keep ones that don't use power. And if you die from no essence, then you lose everything.