Chrono Trigger and Grandia 2 come to mind.
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Xenogears for the PS1 had one of the best combat systems I've ever played. Tied with Star Ocean 2 for the PS1. There's a remake which I think they overhauled the combat system, so I'm not sure if it still is as good as the first edition, but the customizability was amazing.
After that Grandia was fun, but I played it far less than the aforementioned, so have less to say. Chrono Trigger was very good for what it was, and IMHO was only matched by FF6 in that category (heavy turn based combat systems). Chrono Cross is an honorable mention in that category as well.
Lastly, very recently the Sea of Stars game had a very good combat system.
Ultimately these games have great stories, and that's all I really cared about, but the combat systems could either make or break the monotonous grind to get to the plot points, so they had to be at least decent to make the games playable.
I highly recommend any of these games. Chrono Trigger in particular is highly regarded as possibly the greatest JRPG of all time, and personally I'd put Xenogears at 2nd place, with Star Ocean 2 at 3rd. But I might just be nostalgic.
FF6, or more recently, Battle Chasers: Nightwar
I like it old school.
I haven't played many JRPGs, but I'll say Grandia 2. I liked the way the timers worked, and the cancels. Also positioning always adds depth to combat.
Panzer Dragoon Saga was pretty cool too, with the circular movement.
The more I play, the less I enjoy games that have active combat systems, from the Mario RPGs' timed attacks to even Final Fantasy's ATB. I really want to have time to think my turns and just select and use the skills, no reason to try to make it more action-based. So the MegaTen series and Trails series are the ones that cater to my current tastes.
I'll take persona, although it's been way too many games with the same setup. Ditto for the Trails series.
Honestly, I don't think it got any better than ATB systems in FF 6 and 7. Everybody else is either riffing on those or spending so much money they think they can't be those and need to be Devil May Cry instead.
Grandia series. I'm partial to the leveling systems but the battle system is fantastic. There's ATB, field movement, charged attacks/magic incantations that can be canceled, a light combo system. I just love it
Turn-based: Bravely Default. A stellar evolution of FF5 that gives you so many toys to play with, and the titular Brave/Default mechanic opens up a lot of cool ideas just by giving you flexibility in when to take your turn. Specifically BD1 and Second though, I felt like BD2 was a massive step back by trying to introduce a turn order system at the expense of no longer queueing everyone together at once.
Action: Tales. Hard to pick just one, and there are still a bunch I haven't played, but I think I'll go with Vesperia specifically for all the advanced tech it allowed for.
Honorable mention to CrossCode as well, but I know someone's gonna debate whether it counts as J or if it's just sparkling Secret of Mana.
secret of mana was good but honestly seiken densetsu 3 improved on it so much.
on the other hand, earthbound combat is so nostalgic to me.
There's no other system that quite captures the feeling of, "Shit, that was a lot of damage. Do I try to heal them before it rolls to 0 or just spam attack and hope to end combat before they go down?"
Been having a ton of fun with Granblue Fantasy Relink!
Persona 5's combat is really good, although I feel like it's less fun against bosses where you're not constantly getting weak point resets.
The Xenoblade games have fantastic combat, I'd probably rank them XBC2(late game)>Torna>XBC3>XBX>XBC2(early game)>XBC1
I love this. Lookin forward to future XBC games even more now.
I liked the puzzle battle style of games like Disgaea 2.
Not a big fan of the classic "let's all stand face to face and take turns bashing each other" approach.
I agree, throwing enemies into stacks is much more amusing than everyone just standing around.
Miitopia is as simple as it gets
Since FF 6 and 7 have already been mentioned, I'm going to give a honorable mention to Shining Force.
Radiant Historia
The enemies are placed on a grid and your characters have abilities that can move them around or place traps on certain squares, plus as part of the game’s time travel theme you can reorganize the upcoming turn order. Use those together and you can arrange the absolute sickest combos, knocking everyone into a big cluster and then wailing the shit out of that cluster.
Just be sure to play the original DS version and not the enhanced 3DS version with new art, voice acting, and story additions that ruin the tone.
Do the Mario RPGs count
I like the timing-based mechanics because they make the fights feel less like glorified menus. Sure menu-based fights can be strategic and entertaing, but sooner or later you'll end up in grind city just mashing the confirm button to see number go up. Not a thing in the likes of Paper Mario and Bug Fables.
If we talk Action JRPGs then i guess it's Drakengard.
Protagonist power not enough? Then i summon my legendary dragon and end my turn!
(Wait no, that last thing is not entirely true.)
I can't say I have a favorite, but I do strongly favor anything strictly turned based. I've been playing Divided Reigns and its combat system is stellar imho, so there. Lots of weapon types, lots of attacks for each types, lots of skills, lots of magics. Makes non magic users at least as satisfying to use as spell casters.
Legend of Mana, although it was broken, I never got bored with encounters. didn't have to worry about items or mana, only health. if they added a mana system (ironic) and fixed the stunlock, would've been more balanced
Phantom Brave because it's so unique, Chrono Trigger of course because it's so classic.
Ys: Seven and Ys: Memories of Celceta.
Vagrant Story had a really cool swordfighting system.