The materia system is brilliant. Limit break system though... I suppose most of the final ones aren't worth the time it takes to fill them up. But overal, throughout the game it's a good system.
10's battle system is good, but I dislike the sphere grid system and prefer a level system. I think FF9 has the most balanced combat system out of the 3D FF games. The trance system kinda sucks though (the exact effects are vague and you hardly have any time to experiment with the possibilities).
Hmm... FF6's battle system is probably the best one. It has a varied cast of characters that are all very different. Sabin with his combat techniques, Edgar with his tools, Terra with her summons and transformation, etc. Yeah, some standard ones, but a lot of them deviate from the standard as well. Most of it was in FF7 in the form of materia, but I think it works better with dedicated roles. That, and this is just awesome:
Read the mania: http://www.fanfiction.net/~nonexistinghero In SA2, it's Super Sonic and Hyper Shadow.