I still don't get the Idea that you don't have an Idea of the Xenosaga full story, really. The story they told was rather complete, or at least the story that was told, not so much what was originally intended.
Xenosaga was, basically, the struggle against Wilhelm's plans. By games end, I fully understood what Wilhelm wanted to do, and why he did it. Hell, I could even sypmathise with him. I understood the nature of The Testamants, and why groups like The Cardinal Fleet, V-Tech, and Dmitri were all involved, as well as understanding all of their motivations and why they were nescessary to the plot.
It may be vastly different from Takahada's original vision, but as a story on it's own, I don't see what was cut from the main plot. (Though again, some of the other elements of the worlds, like the Realian story, seemed saddly pushed to the side.)
That may be the only thing that boggles me about what you are saying.
Edit: Perhaps the problem here is the term 'Cut' doesn't really apply here, considering how much was probably altered entirely.