I'll probably be labeled a blasphemer for this, but The Saboteur handled character ability unlocks better than SR3. In that game, you have to unlock the ability before it becomes available for purchase, instead of just being Experience Level related. The catch is, each of the bronze/silver/gold Abilities in Saboteur are unlocked by doing something which the next ability would make significantly easier. I'm not remembering the exact progression, but it might have been "Get 20 headshots" for "Reduced recoil on sniper rifle," whereas the next stage may be "Get 5 headshots in 15 seconds" for "Sniper rifle reload time is halved."
SR2 gave automatic, free unlocks for doing specific tasks. e.g. "no falling damage if you nail a BASE Jump perfectly" -- it was actually closer to the model where progress is related to what you've done, not just how much you've done and how much money you've got.
OTOH, Saboteur ran out of unlockables and ways to spend my money well before I was ever finished with the campaign...