Yes, chaos was being implied as Jesus. The name "Yeshua" is even another name for Jesus, but no he wasn't Jesus Christ in the Bible, it was mainly an allusion. Wilhelm is basically the opposite of chaos, and his motive was basically to reverse time, also
this article can do a lot better job of explaining things about him than I can. Another way to look at Wilhelm, is to think of him as Xenosaga's Krelian.
The ending was pretty much closed, but just enough was left open if they wanted to continue the story further, like Shion and Allen's search for Lost Jerusalem (Earth) which could be tied in a sense to Xenogears, though not directly. Any future Xenosaga titles depended on Xenosaga III sales and demand from fans according to a Namco Bandai rep and Episode III only sold 343,000 copies according to Namco Bandai's quarterly sales report, so who knows we may see a future Xenosaga title, but I was fairly happy with the ending.
Did you enjoy the game and series as a whole though? I know I sure as hell did, Episode I was a great beginning, Episode II while it focused too much on Albedo and Jr, was still very enjoyable, but easily the weakest of the three, and Episode III was nearly perfect, the battle system was a nice mix of Episode I and II's and the story was extremely well written and paced. I really should play through Episode III again.
