JRPGs tell the best stories you can find in any medium, and Xenogears specifically is the very best the genre (and storytelling of any medium) has to offer.
It explores the philosophical ideas of Friedrich Nietzsche, Sigmund Freud, Carl Jung and Jacques Lacan, it delves into the nature of God, The Universe and existence, the nature of human memory, the struggle between man and machine, the horrors of war, ethics, politics, economics... the list goes on, and it does so with such detail and scope.
But beyond that it's quite simply just far more complex (complicated subject matter, complicated narrative, so much shrouded in mystery and ambiguity, with plot twists that make you question everything you had been lead to believe about the game's story) and compelling (helped considerably by its phenomenal music, as well as the fact that it touches on just about every single emotion of the player) than Planescape: Torment, and the same's also the case with Chrono Trigger, Chrono Cross, Radical Dreamers, and the Xenosaga series.
Just because someone wrote it on wikipedia doesn't make it true. The game is still shallow when it comes to tackling these phenomens. And another thing is interpretation, you can pull Freud for any bullshit that comes to your mind, I can write essay about how Kratos is a deep and complex character. Nitezsche's work have not been yet understood and Jung's archetypes can be applied to absolutly anything.
You've made it sound like if Xenogears were the final product of the whole western philosophical tradition, which they are not.