Every system has ways of showing the progress of skills exhibited by a user.
Mine will not be very different.
The more the MC uses skills and becomes adept at using them, the more XP they gain.
Every 10 levels, skills acquire something that makes them more useful/powerful.
Every 50 levels, skills evolve to a superior version, acquiring something that makes them more useful than its anterior version.
The MC can also level up, either by achieving missions issued by the system, or by filling the required conditions of hidden achievements.
These achievements can grants skills, XP, items, or titles.
Every ten levels, MC has a free random item, going from [T] to [CR].
Every level-up heals the MC of anything he suffered until then.
Skills are not used through the system, the MC comes to know how to use them even if he acquires them through something other than training.
Skills can be acquired through repeated actions.