Just a few quick suggestions about the Cmbat Simulator Augment. I never tried that augment before, but now I quite like it.
You should add a shield training simulation since it's strangely left out, all you would have to do is spawn a simulated ship with a laser weapon that fires just fast enough to constantly pelt your shields, but never actually penetrate more than one layer.
For the combat simulator another less lethal scenario would also be to spawn a simulated AI ship that you can "board" and destroy it's systems. Destroying each system completely would damage the ship just enough so that it would surrender and end the simulation. Allowing you to pull your crew back and preventing the non-existent ship from jumping away with them.
Of course that would require a teleporter. But, the combat AI's can actually be quite lethal, as we all know... Engi's would be a better opponent, but that kind of breaks the lore of the simulation.
So one other alternative would be to spawn a simulated AI boarding ship with an "invasion" AI and normal teleporter of two that the AI's use instead all spawning on your ship at once. That way it is much easier to get an advantage over them since you will only be fighting two at a time.
Lastly, the fire on the repair simulation is interesting, but if you just removed that you wouldn't need to have the warning that it could actually damage your ship. I don't think the fire is really necessary...