What kind of skill system would be better?

1. A system where players buy skills/magic from a skill shop.

2. A traditional system where players earn skills/magic by leveling up.

3. A system where players buy skills and earn magic by leveling up (or vice versa).

it all really depends on the feel and the storyline

for example: if magic is rare in the world and only a select few know it, the store would be impractical and completely out of the bounds of the world.

the third one, well because pokemon rules.

I would go with the 3rd one......but the other two have that classic feel to it

There's more magic in the world than skills, so I'm thinking skills should be learned, and magic could be purchased. However, not every character can learn every magic. Would that be good?

yes that would be superb