I think Skyrim has the best progression system and I think you should work work towards class specific specializations. Example, a hunter could become a full on Sniper, a saboteur who relies on preemptive thinking and ambushes, an infiltrator who relies on stealth and hit-and-run tactics, or an assassin who specializes in attacking a singular enemy with great damage. I think there should be no perks and that abilities should be based on the equipment used. If you wanted a active camo type ability you would have to use a piece of armor that achieves that effect. Specializations would give you passive boosts like a Sniper would have increased critical point damage, a saboteur would have a bonus suprise attack damage, an assassin would have increased damage when focused on a single tareget, and an infiltrator would have increased stealth.