Ah, what a grand topic!
Masato Kato was on Xenogears, for one thing (thanks to ZeaLitY for pointing this one out I think):
Xenogears (1998): event planner, script writer, lyricist
So I would greatly suspect that the floating kingdom of Shevat was inspired by Zeal. I'm not sure what the original names for the Three Sages were in the Japanese version of Xenogears; taken in their English context alone, it would be quite easy to say the Three Sages = the Three Gurus, but I don't think Kato named the Gurus Melchior, Belthasar, and Gaspar in the Japanese CT script. Unless I'm mistaken? I thought they were Basch, Bosch, and something...but goodness, what an awesome job Woolsey did with the names. I mean, Sara = Schala? Brilliant! You can say what you want about Woolsey's mistakes, but I adore the names he came up with.
I am a firm believer that Lavos is an interstellar weapon that possibly destroyed its creators before going on to conquer the universe, a la Deus. But to say that Deus built on the Lavos concept is premature, since this has not been addressed by Kato himself, and Tetsuyah Takahashi probably came up with Deus independently. 'Tis within the realm of fanon only.
I, too, heard the rumors about Xeno = Chrono sequel, but I can provide no info to confirm or deny them.
*Was anyone impaled or otherwise stabbed or greatly injured in Xenogears?*
-Ramsus stabbed Miang, did he not? This is getting creepier by the moment...Kato strikes again!! But nobody was stabbed in CT, correct? Cyrus was burned to death, and Crono was vaporized though.