Legend of Dragoon. It's an RPG where all your characters can turn into badass dragon warriors, the story was magnificent *spoilers* with Rose (the carrier of the team in the beginning) being revealed as trying to kill Dart and destroying his town in the beginning (essentially setting the game into motion). Interesting party members get killed off and you can recruit a recurring bad-guy into your team. Also the only game in which it indicated how close you were to an encounter (green-yellow-red indicators above your character),
The game is incredibly varied with character development. But the battle system is what takes the cake - each time you attack you can press a button at a specific time to build up an "addition" to your initial attack. Once you complete the combo, a special is unleashed that decimates the enemy. Your attacks can level up when used (like in the Disgaea games)(also why Rose is so OP in the early game) along with normal RPG elements of elemental attacks, stat building, and equipment management.
Lloyd - the games antagonist - has probably the second-most interesting character development and storyline (behind Sephiroth). And you eventually get his Dragoon spirit, which comes from the Divine Dragon (easily the most impressive boss fight for an RPG to date).
So yea, character deception, amazing visuals for the time, combos, Dragoon-form, character death, amazing antagonist, and varied world (granted little linear) and a gameplay experience that lasts MUCH longer than today's RPGs - I can would easily call this in my favorites.
Also you travel to the Moon.
