After reading the OP my first thought was some kind of job master or class mastery merit system.

Personally I am always partial to the systems that after you reach cap allow you to gain points with XP. Starting with a very low cost, and scaling in cost for each point. The poinst then used to by specific stat upgrades, Job master abilities that can be achieved only with JM abilities, or purchases that allow for expansions to already existong abilities.

Just an idea from some previous MMOs with decent systems I liked.