Compare positioning in any Final fantasy to Valkyria chronicles, or any turn based WRPG. Can you honestly tell me the positioning in most jrpg turn based games is on the same level?
First off, apples to oranges. Classic turn based JRPGs are very different beasts than Isometric RPGs, they are closest to wizardry than BG which all that it entails.
But answering your question, yeah, I can think a few. The whole genre of japanese TRPG, from Tactics Ogre to Disgaea, passing through Vandal Stories, Final Fantasy Tactics and Devil Survivor, you have tons to pick there. There are also many JRPG where characters move through an arena using AP to decide how far they can move and have different ranges for their attacks. If I have to pick an example of a really good one, look at Breath of Fire Dragon's Quarter. There you can put down traps before starting combat, and positioning is so important that choosing between a stronger sword or a longer sword can be quite difficult, and skills that push or pull enemies are the most useful of the game. Of this kind of JRPGs with AP systems you can also find more niche things like Eternal Sonata. Then you have Trials of the Sky and Cold Steel series, both have combat system that include movement and positioning. Then you have more strange and unique game like Resonance of Fate, which is pretty much an action movie made TB JRPG where the combat system is all about positioning, running through enemies and taking cover to avoid being shoot at. On the other hand you have single character RPGs like Vagrant Story or Parasite Eve where moving around and controlling your opponents position is also really important. Then you have shit that is almost real time like the Xenoblade series where attack has positional and ranges, and getting the fuck away of the enemy at the right time can be the difference between dying or winning a fight.
Those are really just a few examples. I'm sure others have many more. Also who the fuck but the most ignorant claims that the main line Final Fantasy games are the pinnacle of JRPGs? And even then you have shit like FF XII which is RTwP and range matters when it comes to combat, so even there you have cases where positioning matter.
PS: Oh yeah, forgot to add that even some FF have quite a lot of customization. Final Fantasy I, II, III, V, VII, VIII, X and XII all have either party creation, job systems or classless systems that allowed you to customize each character role in the party.