Dude, that's the POINT: anyone with a year of Western Religion courses and a smattering of philosophy could pen Xenogears' plot. For all of its pretensions, the ham-fisted attempt at allegory is meaningless -- the fundamental plot is still pure anime tripe that just assigns fancy names from Catholic, Mithraic, and Hindu mythology to various ill-explained pieces of machinery (be it giant robots, weapons, or genome projects) and then waves its hands about the ascension of the human race. It's just an Eva fanfic with a little more time spent at the encyclopedia. Hell, it even has the wacky anthropomorphic sidekick, the predictable magical girl, and the superhuman boy hero trying to find a purpose for his existence. It's a giant reeking cesspit of anime cliches cutely doctored up by invoking such deep sounding and nebulous (to an outsider) terms as "gnosis" and the mythologies of Ur.
As hard science-fiction, there's no thought driving the allegorical relationships between the invoked mythologies and the technology. For a real example of how this sort of thing should be done, read (if you can stomach it) Steven R. Donaldson's "Gap" quintology -- as darkly depressing as it is, it's the sort of tight mesh between deep allegory and proper hard science-fiction that stuff like the Xeno* titles and even Evangelion would LOVE to achieve.
Proper allegory requires understanding the originating mythologies and religions in depth. Xenogears just name-drops at the literary party and gets fanboys THINKING that they're hangin' with someone clever. Xenosaga is even worse -- when Takahashi ran out of mythological references, he started getting slaphappy with the military-sounding acronyms. Yuck.
In the end, though, Xenogears is just another by-the-book anime sci-fi plot about the ascension of the human race with no real science or consistent mythological data to back it up. It's more about the chance to show off flashy-looking mech designs or exotic superpowers trumped up with cool-sounding names than a legitimate attempt to explore the source material and/or the future of science and human advancement. THAT'S why it's shallow.
