A learning by doing system can also make character development extremely unflexible as you cannot switch easily or at all. Especially bad when your level 1 and 2 skills are kinda bad, but it becomes better at level 3.

It can also lead to exploitation and grind. E.g. if you gain XP by hitting targets. You might want to fight with weak weapons to hit more often. Or fight against a selfhealing enemy, to max out the skill faster and so on.