I think skills had become to game-breaking in Fates, especially with the My Castle feature. Players tends to create over-powered gods by buying skills and reclassing.
In my opinion, a skill must have a cost (HP, debuff, whatever...) and the player must not be able to trigger it at each round. It must have a strategical use not a game-breaking one. Echoes does it better in its own way.
Class locked or weapon locked skills with a cost and triggerred by the player seem to me a better way.