Yep, there are definitely some connections. Tetsuya Takahashi actually said in an interview that Xenogears was intended to be CT2 early in the writing phase--though who knows how much influence that had, since according to Kaori Tanaka the story took a pretty tangled course during development. Anyway, for those that have played CT and not XG, here's a rundown. (Note that these are major spoilers! You are ruining some of your potential XG experience by reading further!)
-In XG, a intelligent planetary-invasion weapon ends up marooned on a planet and creates a base population of humans with the intent of absorbing the population after it has multiplied in order to repair its damaged biological parts. The Lavos parallel should be obvious.
-XG's Shevat is a lavish, matriarchal floating kingdom featuring New Agey Yasunori Mitsuda music and three key scientists or "sages" named Melchior, Balthasar, and Gaspar. Postings on Tanaka's FRIDGE confirm that this happened because Masato Kato worked on both games. (Oddly enough, while CT's gurus were Hash, Gash, and Bosh in Japanese, the Sages of Shevat had the wise-men names on both sides of the Pacific, as far as I can tell.)
-This is a stretch, but XG has a really important event at the end of a "ominous enemy stronghold" area, then has the stronghold change form and uses a "remixed" version as the final dungeon, just like the Ocean Palace and the Black Omen. The difference is that you don't actually play the dungeon the first time around. However, there are a lot of dungeon-like areas that are glossed over in cutscenes on XG's Disk 2, and a lot of other evidence points to budget or time constraints affecting Disk 2's production, so who knows if it was intentional.
