Despite FFXIII having alot of problems and not being all that great overall, I think it's battle system struck a pretty good balance between simplicity and depth. It was simple and elegant, could be really tense during tougher battles, looked cool, and I thought that switching roles in different paradigms was a perfect acceptable (and maybe even better) alternative to not controlling every character in your party (which alot of people complained about) . I thought that the leveling tree was kind of tedious and pretty darn restrictive, but the gameplay itself was great and the action unfolded at an optimal pace. It's too bad that the easy battles persisted too far into the game and the lack of anything to do other than fight and watch cutscenes eventually gave the battles a feeling of tedium. If they would have paced the game better and had you perform other tasks between combat stretches and ramped up the difficulty earlier, I think alot more people would appreciate the simple yet strategic battle system.
As for the worst? FFVIII. My God, the junction system sucks! It shows everything that is wrong with convoluted battle systems that are convoluted just for the sake of being convoluted. No, it wasn't innovative because innovation implies that thinking outside the box actually leads to pragmatic results. Thinking outside the box just for the sake of it is pretty much game design masturbation IMO, which unfortunately, the FF developers have been guilty of on more than one occasion. The junction system is just needlessly complex, counter-intuitive and lacks balance. Leveling up is not advantageous, yet the system can be easy to exploit. And there is the horrible drawing aspect. At the end of the day, it just felt like FVIII's battle system was a bunch of parts that didn't mesh well with eachother. Some people may like this system for whatever reason, but there is the simple reality that alot of people are atleast initially confused by it, which does not speak well of any battle system. Not to mention that the tutorial is crap.
I suppose I could forgive a convoluted system if it ultimately leads to depth, but this doesn't really happen in FFVIII.
I don't think FFVIII is bad overall (though it does have alot of chinks in the armor) and I do find it to be one of the more beautiful FFs, but I do think that the junction system sums up the game's worst quality: awkwardness.