This is pretty late, but I never did wrap up my impressions of Xenosaga: The Animation. Maybe it's because I know nothing about the game, but I found the entire affair kinda confusing. A lot of it didn't seem to make any sense at all.
By the end, I was pretty much just watching it to see Shion wail in anguish, to hear Mary bitch someone out in that cranky voice of hers, and to see KOS-MOS beat people down.
Shion just doesn't understand KOS-MOS' genius.
Spoilers about the last episode: Am I seriously supposed to believe that KOS-MOS shouldn't be expected to survive a fall from orbit? After the ass kicking she gave to pretty much all of Creation this series, five will get you 10 that KOS-MOS can survive the End Times and/or the universe finally collapsing in upon itself.
And just exactly what did chaos do with the glowy hands thing? I initially assumed it was a lead-in to the game's sequel, and not anything to do with something I completely missed during the anime. However, based on what I've heard about the games, that isn't exactly true either.