From a design perspective, I think you could safely pick anything from V to XII and say it's the best one, honestly. VI and Chrono Trigger really stand out as the most refined in terms of game design and systems from that particular era.

Without spoiling anything, the episodic storytelling style is taken to its limit in the game's "part II", and it allows for some really clever writing. VI is one of those games that kept me thinking long after I finished it.