there are no issues with the Xengoears licence, and I woudln't be surprised if Namco really DOES own the Xenogears licence. If they had to be careful, then Xenosaga would not have had TWO things from Xenogears in it.
Xenosaga 1 had both Zohar, which is from Xenogears, and Abel, who was the first incarnation of Fei, and looked just like Abel was supposed too. Either Namco owns the Xenogears licence, or they and Square have an agreement where Square doesn't care.
As for the story, no one can say what it will bring. All 6 episdoes in Xenogears were detaield in Perfect Works, the 300+ page art book/companion to Xenogears. Xenosaga 1 loosly followed the outline for Episode 1, Xenosaga 2 isn't even CLOSE to the what Xengoears episode 2 should be. Xenogears ep. 2 would take palce about 12 years after the eldridge crashed on the planet, Xenosaga 2 is taking place before that event, assuming that even is even going to take place in the Xenosaga timeline.
it's hard to say where the series will go. I do think it's obvious that Namco and Monolithsoft either own the Xengoears licence, or have a deal with Square.
For reference, according to Perfect Works Ep 3 would take place 4000 years after the Eldrigde crash, during the Zeiobem civilization, who created Emerelda. Ep. 4 would take place during the great war 500 eyar prior to events in Xengoears, ep 6 would take place shortly after Xengoears.
and Grey Ninja, you're an idiot. Not buying a PS2 or PSX just because it's not Nintendo, sorry but that's just sad.