Just add movement.
Add spaces that characters move in and add resources for moving and taking other actions.
Then of course overhall your abilities: make AoEs take the space into account, add cover/LoS mechanics, make hybrid abilities that move/attack/deal damage/deny areas at the same time.

I too don't understand why JRPGaylords are so afraid of positioning in a 2D or 3D space mattering in their games.