I know you added per-action familiarity in place of skills, but maybe you could have both? (Skills being rather minor progression compared to per-action)
As it stands, I have had a couple runs where I take a break and forget quite what I was doing and just head the wrong direction or do something that is effectively irrelevant by the point in progress I have reached. If skills still existed, it would feel a bit more like I still made progress.
It also makes sense narratively. If I tear down a solid metal door, I might not be ripping the next one down with my bare hands, but I'd definitely have some degree of awareness where to start. Same with the various hackings -- theoretically these stations were built to some standard, so learning how to abuse one's digital systems would give insight into the others'.