I've played through Xenogears 3 times and Xenosaga twice. I'll be sending in more submissions on their connections in soon. Excuse my bad spelling. And watch out for my spoilers if you haven't played XS.
Probably one of the most peculiar connections between these two games is the remarkable similarity between these 3 completely different things. As anyone who's played Ep. 1 knows, KOS-MOS is supposively the ultimate anti-gnosis weapon, almost based off designs of Proto-Merkabah (Merkavah). Deus, the ultimate inter-planetary assault weapon was created with the Zohar at it's core. Since the Gnosis are attracted to the Zohar because of it's elevated status as containing a fourth-dimensional being, this would imply that Deus could have be created by luring Gnosis using the Zohar. Then using some sort of weapon or device (possibly KOS-MOS), capture and use the power of the Gnosis. Several parts in the opening cinematics imply KOS-MOS is somehow related to Dues.
1. When Deus, supposively starts taking over the ship because it realised it was being disposed of you see the image on screen of when the girl in the bridge of Eldridge is trying to keep Deus from spreading. Deus has tapped into the net of the ship's computer and she tried to stop him by cutting power. In XS, when KOS-MOS uses the Hilbert effect inside the encaphelon device, she starts creating a neural net within herself (I think this is when it happens...), further enriching her already existant programming. The two computer screen images are similar.
2. When Deus has comlete control over the Eldridge, the screens blank over and all they say is "Ye shall be as gods." This is KOS-MOS's start up code.
3. Deus looks a lot like a Gnosis
Then you add U-DO into this mix. U-DO is a galactic phenomenon with a consious, that's supposively suppose to destroy the universe. We probably won't find out til Ep. 2 comes out. I believe since KOS-MOS is suppose to battle U-DO, she succeeds and captures the power. The Council members from XS see this as an opportunity and use the Zohar to lure Gnosis while using the KOS-MOS/U-DO to absorb them.
Then there's Albedo, a U.R.T.V, who was sent to battle U-DO but came in "contact" with it and became a perfect chain (something to do with nanomachines?). This guy just creeps me out, seeing as how he rips off his own head and grows a new one. I had a theory on how Albedo was related to Deus, but I can't remember it. I do remember that Albedo is trying to get something from Shion Uzuki, but KOS-MOS is blocking him. The head of vector (Wilhelm?), obviously knows there is something special about Shion. I need to play through XS again.
Shion, Jin, and Shitan Uzuki
This is a tough theory and I'm not quite sure about it, but Jin seems to be freakily similar to Shitan. Both are too curious for their own good, are swordsman, and look identical. Now obviously, if something as important as Eldridge went down, especially with Deus on it, after 10k years, someone out in the universe has got to notice, unless it was some sort of Exodus and Deus was a back-up system to make sure the people had some sort of extra protection. If that wasn't a last ditch effort to save their race (running from gnosis???), then I think many years before someone related to Shitan/Jim/Shion was sent to the planet to moniter what was going on, but eventually the objective was lost (Solaris' brainwash?)
I'll be posting more soon.