McFlabbergasty said: I am leaning towards the Morrowind style of leveling up, where you increase a skill level by performing the action(s) associated with the skill.
Ah! I used to really enjoy playing Morrowind. That system sounds like a good one to use.
Have you considered a set of ESP skills or do you not wish to venture into that sort of territory? Your mention of Morrowind brought magic to mind, and while some of your proposed categories have obvious affinities with Morrowind's skill set (e.g. bypass for security -- great name for the category, by the way!), there is little to take the place of magic. Perhaps this is intentional though. I confess that I'm not really sure what an Indie action movie is.