Either Final Fantasy II or XII.
Final Fantasy II is bit rough around the edges, nevertheless its leveling system was way before its time. Modern games like TES V: Skyrim and Fallout: New Vegas utilize it today although a lot more refined. First FF to have fleshed out characters.
Final Fantasy XII on the other hand was a breath of fresh air long after series became stale and predictable. It was a perfect mix of science fiction and traditional fantasy. None of the worlds before looked as beautiful and diverse as Ivalice. Distinct lore enriched by another great game in the series, FF Tactics. It introduced down to earth characters, some of the best NPCs out there, a brilliant villain ever so determined, one you could somewhat even empathize with, who actually did what he intended to do. Gone was finally a cheesy teen love story in favor of something more subtle. Non random battles, full scale world map, not to mention hardly any FF had this much content in terms of items, weapons and equipment. You had freedom to define how your characters would develop. Its strongest point though is just how customizable the AI system is, you could take complete control or adjust AI to work on its own, more games should have this.
Few years ago I would add FF IX to this list, but that game got insane amount of recognition. It holds highest score out of all FFs, it's Hironobu Sakaguchi's favorite title, saying that it's closest to his ideal view of what Final Fantasy should be. Only after I joined TFF I realized just how many fans it has. Sadly some still refuse to play this game due to its lighthearted design even though the story is all but lighthearted.
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