The games I listed as well as being among the most deep and complex stories are also among the most emotive ones as well, helped incredibly not only by incredible emotive storytelling but incredible emotive composition by the man who does it best: Yasunori Mitsuda. His works on the Xenogears, Chrono and Xenosaga series are nothing short of remarkable and the very best that are out there at drawing out the audience's emotions.
Planescape: Torment really doesn't have that much more to offer than any other Bioware/Black Isle/Obsidian game, its only real differentiating factor being its fantastical, and quite frankly weird setting.
Xenogears is quite simply a more advanced piece of storytelling. Its story is far deeper (far greater quantity of themes and detail with which the themes are explored, these include deep philosophical, religious, psychological and political themes, and it actually uses some of those themes as the very foundation with which the story is told (God is Dead, The Slayer of God, You Shall be as Gods, eternal recurrence, the Overman)), far more complex (complicated subject matter and narrative, an abundance of mystery and ambiguity, seemingly unrelated events connecting together in a manner that thematically fits, revelations that make the player question everything they believed they knew about the story up until the mentioned revelation, a tonne of symbology). It's perfectly acceptable that you may prefer Planescape: Torment, but at least admit that Xenogears is at the very least a more intelligent and advanced piece of work.