In a 2003 Game Hihyou magazine interview with Xenogears and Xenosaga Episode I's composer Yasunori Mitsuda, he was asked if he would be back doing the music for Xenosaga Episode II. He revealed that he turned down the job partly due to other projects he was working on, and partly because of creative differences when his planned compositions did not match up with Namco's concepts for the game:

"No, I’m not. I had to turn it down. Partly it’s because I’m very busy, but the bigger issue was that I set some goalposts for myself and said, “ok, I want to do this kind of thing for the next Xenosaga.” But my ideas were too far apart from the vision that Namco had for Xenosaga. I had started conceptualizing the music with some of the Procyon Studio members here, and we had even laid down some ideas, but once I realized it wasn’t going to fly, I had to turn the work down. I apologize to everyone who had been hoping otherwise…!"
Contributed by ProtoSnake