I hate to say this, but probably the best completely turn-based battle system is FFX, though I have yet to play even Xenosaga Ep. I to completion, less yet Ep. III which I hear is the 2nd coming of christ as far as JRPGs are concerned.
Now if we're just talking turn-based in that their are turns, as opposed to a real-time like a Tales of, Star Ocean, or Kingdom Hearts, that's a wide open question, but I'd say overall when it actually came to fighting (we can talk about managing characters later), FFVIII was completely badass because it was such an utterly broken fuck fest of destruction* that practically anything you could want done is yours given you're prepared to do it. Always get the first turn? Alert, boom. Make your time bar fill so fast it makes playing on the highest speed practically dizzying? Auto-Haste and Speed+80% it is. Easy, constant access to limit breaks? 99 Aura spells, go for it. Mug with full attack damage? Yes. Stats so preposterously broken you wonder how in the world you could ever conceivably lose? Junction Ultima, just do it (of special note, health in the multi-thousands is VERY easily achievable probably 5 hours into the game after you get Siren in Dollet). And keep in mind a lot of this was attached to easily the most badass animations of all time when the game launched, and some great battle music. Say what you will about draws, the results are glorious.
And it's not a boring kind of ridiculousness like FFVII either, which could be reduced to KoTR with Mime. You actually get better results with speed buffs and a good str junction than Eden, which, mind you, can break the damage barrier. At his most ridiculous, Squall easily hits with more power than characters that are considered outright gods in other titles, even without using the trigger mechanism, your attacks will probably be doing 9999 damage every time if you have the Lionheart and a decent Str junction.
* And remember, every good JRPG at some point is an utterly broken fuck fest of destruction, so don't ever count that against it.