I'm curious of peoples opinion on this.  My opinion is split between the evolving Tales combat system, Tales of Vesperia is my fave of them so far, and Final Fantasy XII.

People can argue for turn based systems or against.  Most of the time the "non turn" based system is actually turn based but hard to tell when its an active turn based system.

That said, most people seemed to dislike the combat system of Final Fantasy XII, yet I think it was if not the most one of the most innovative systems thus far.  Allowing you to build smart AI character actions via the gambit system or hunker down and issue commands per active character.  You could build up your sub characters to do fight how you wanted but completely control every action of the main character.

I liked Vesperia because of the combo system and the use of combo linking to create hundreds of combos.  The Tales series should get applause for finding a good system and continuing to evolve it in each game.

I like the Mario&Luigi combat system, Have you tried it?

For me, Paper Mario: TYD has one of the most innovative RPG systems out there. It's turn-based, but there are different action commands that you have to do. Plus, I love the audience and how they react to the current battle.

Yeah. I wouldn't say it was horrible.  Definitely was an interesting experiment to cross mario platform with turn based rpg elements, but it ended up being kinda bland.

Vesperia is close to the Star Ocean one, so its not that much of innovation , i say

Valkyria Chronicles : i didnt remember anyone did that before.

Chrono Trigger : The Team Attack thing (Forgot it's name sorry) is very new at those times.

Shadow Hearts : Cant find that system outside shadow hearts.

Grandia series is #1, its both real time and turnbased

persona 3, suikoden 1, legend of dragoon

i'll second valkyria chronicles

TWEWY hands down.
Althought I didn't like the game overall.

thousand arms ps1.(worst battle system ever , but i just love that game)