First, let it be said that I think that no one could have outdone Mitsuda's score for the first game, except maybe himself. It sits among the best soundtracks in my collection along with John Williams and Howard Shore.
That over and done with, I also have to say that Yuki Kajiura wrote a completely differet sytle (and therefore mood) of music for Xenosaga Ep. 2 than Mitsuda created for Ep. 1. But the second part of the series deserved a retelling through music. Mitsuda took great advantage of a full orchestra, while Kajiura makes use of electronics, a small selection of strings, woodwinds, and especially pipes. A whole different world is introduced in the second part of the series, and Kajiura's difference in style helps to throw this transition into sharp relief.
Character themes are altered or changed. Albedo's once erratic and off-kilter operatic theme song (used to represent his less-than-sane state of mind) is changed at the hands of Kajiura to a soft, menacing half choral/half techno amalgam of terror (used effectively to show Albedo as a menacing character, not just a man suffering from mental instability).
Most of the tracks on the soundtrack are superb, showcasing Kajiura's expertise with themes and altering them, mixing them. There are a few tracks, however, that do not stand up to the test. For example, the first "Battle of the Elsa" track is a dissonant and indecipherable piece which I skip on every playing. Along with the uneventful track "R&D Report," which shows about just as much emotion that the voice actor for the main character chooses to display. But, other than the few blips on the radar of unworthyness, the score is one I would recommend for fans of the game, or fans of music in general, if they feel so compelled.
One suggestion: Amazon's prices are extremely high for this soundtrack. I bought mine on E-Bay for $14, a very reasonable price for 2 disks and about 1 hour and 45 mins of music. Happy shopping!