I agree with the OP that being able to level up your retainer is a good thing, as well as a later suggestion that they be unlocked via quests. In my mind, these quests would allow the purchasing of special "permits" allowing the retainer(s) the additional abilities granted by the permit. Further, these permits would have recurring fees in order to continue access to the special retainer ability.

Some additional suggestions I have regarding possible abilities for retainers:

a) Linkpearl to allow talking to retainer. At first allows only viewing of items still in retainer bazaar.

b) Later, allow moving of items between retainer inventory and bazaar via linkpearl.

c) Still later, allow direction of retainer to a specific Market Area without having to "hold their hand".

Given that these are powerful abilities justifies the up-front and continuing costs to get and maintain them (and also adds some additional, needed gil sinks into the game).