...snip...
Sorry, but the link to Nietzsche is fairly tangental.
This article (warning: super spoiler intensive. Summarizes plot. ) explains how Xenogears (not Xenosaga) is heavily linked to both Gnosticism and Jewish Kabbalah (it also mentions that there are a few references to Nietzsche, but there are more to Carl Jung, so take that as you will). Even
Tv Tropes has this to say about Xenogears:
It is particularly remembered for a uniquely convoluted plot spanning ten thousand years, themes cooked out of Gnosticism, Jewish mysticism and Jungian psychology, and an atmosphere that was remarkably Animesque for its time, leading to the game's infamous hour-long cutscenes.
and
Gnosticism: The overall story of Xenogears is an almost exact re-telling of Gnostic mythology. Surprisingly averts What Do You Mean Its Not Symbolic in the sense of how true the game stays to the original Gnostic religion. So many games mindlessly rip names and ideas from ancient religion without grasping the broader context; the creators of Xenogears obviously did their research.
(they also mention the Nietsche wannabe).
So, tl;dr, I'd say that while there are some inspirations taken from Nietzsche in Xenogears, to ignore the fact that almost
the entire storyline is an allegory for Gnosticism seems disingenuous. (itsstillagreatgamethateveryoneshouldplay...)
*edit* Hell, the main enemy in Xenosaga is called the
Gnosis! Not the Nietschites