Combat system: Valkyrie Profile (Lenneth). The system had its flaws, such as having mages being basically the same, and not enough enemies that forced you to use the finer points like feints, over/under attacks and such. However, its pace and emphasis on timing makes up for it in my mind. Then again, fighting games are my second-favorite genre so i might be just a wee bit biased here.
Leveling system: Sphere Grid. No contest. When I first played FFX, the sphere grid seemed like just another gimmick (similar to the horribly un-polished FF8 junction mess). On a closer look, we have a system that is simple at first, but adaptable to your later needs.
For the beggining, it gives you a linear progression to follow with each character, which gives a specific role to each one. Later on, you get spheres that let you hybridize your characters, to make them strong enough to laugh at everything the "normal" storyline throws at you. Even further on, it gives you the tools (like clear spheres) to completely rework the grid and REALLY max out your characters, in case you're mad enough to go against the Dark Aeons or Penance.
