Favorite Song: Uh... dang. I like the whole soundtrack. If I had to pick one... the XS2 opening theme is amazing and set up a lot of variations on it later on.
Least Favorite Song: Second Miltia. Whee Phantasy Star music in the PS2 era. Robot Academy & Records are sadly close seconds, but at least they work in-context. If we're going just from Kaijura's work... uh, this is hard. Every single song on the soundtrack is at least an 8/10. I guess Final crisis, which is still pretty good, but kind of repetitive.
Favorite Stand Alone Song, Worst Stand Alone Song: See above, pretty much.
Favorite In Game use of a Song: Here She Comes (KOS-MOS) was used pretty well. Same with Fatal fight (Jin & Margulis). I like Kaijura's remix of the Song of Nephilim, too. The slowness and erraticness, making it feel more like a solo than something with a conductor, makes it even more eerie.
Worst In Game use of a Song: Second Miltia. It's a bad song and they play it in a pretty darn important place you visit a fair amount. There's also a blackeye to the game for NOT USING KAIJURA'S STUFF ENOUGH. I mean, she wrote some great themes for the Jin-Margulis duels if nothing else; play them during the system battle, too!
Most Memorable Song: Tricky. The regular battle music is the trivial answer since you get to hear it a lot, but eh. Song of Nephilim is a strong contender, but it appears in all three games and also is kind of cheaty. I'll say Sweet Song / the various Sakura themes, even if they're in some ways not as good as the main opening theme.
Favorite Melody: The Opening Theme again, seen in many other places.
Quality of OST: When I first heard Kaijura's work before the game came out, I was actually kinda underwhelmed. It seemed... boring? It certainly didn't have the aggressive vocals that Kaijura's standouts from the .hack, Noir, and Madlax had. And with a few exceptions, it wasn't the bombastic orchestral Wagnerian stuff from XS1, even taking into account that she wasn't writing battle themes.
I put it aside for a bit... and then a friend who's more of a music nut than I listened to the soundtrack and thought it was fantastic. I figured it was worth another listen. Listening more closely, I did like it more. And then I actually played the game and saw it use in context. My major complaint was that they didn't use the event music more - it was awesome whenever it did play. Furthermore... this is one of those soundtracks that not only didn't go stale with every listen, but kept getting better. Reminds me a bit of good classical music that can take one theme and play around with it in 4 different ways; different versions of the same themes for different purposes and all. I'm not normally a huge piano & strings fan, but Kaijura certainly uses them effectively. The vocals are also surprisingly solid too, and it's always backed by strong percussion - unlike some other composers, it doesn't feel like she mailed in the background.
About my only complaint with the Kaijura soundtrack is that it isn't exactly hummable - there aren't many pieces with strong, strident melodies that are easily memorable, unlike, say, Uematsu. Also, since it's a somewhat short soundtrack that plays around with a lot of the same melodies, it isn't high on sheer diversity.
Anyway, as noted above, basically the entire soundtrack is great. There isn't a piece on it I don't like. Being short helps, but this can be said of few soundtracks. (Actually, Legend of Mana, discussed above, comes close - it's also very consistent).
From Hosoe's part of the soundtrack... well, it was actually pretty good in parts, just erratic and having to compete with one of my three favorite current composers. His battle themes were all pretty good. Considering how long and potentially boring many of the regular fights are, the fact that the regular battle theme was quite active and almost pompous was actually appreciated to help keep interest in them. His dungeon themes were decent too. I have a certain weakness for the Ormus Stronghold music (feels almost last-dungeony, then gets remixed once the bomb is set), the MOMO's subconscious pieces were fitting, and the Old Miltia pieces sound vaguely Metroidy - creepy and empty. (Side rant: Why the heck did you fight no Gnosis in Old Miltia and only U-TIC robots and stuff? Didn't the Gnosis destroy Old Miltia and there's actually a solid plot excuse for them to hang around? ...whatever.) So yeah, Hosoe can do dramatic and/or creepy, but anything happy he failed at with only a few exceptions.
Other Thoughts: Why didn't they have Kaijura do the whole thing? Well, they fixed that in XS3, at least.
Overall Rating: Combined? 9/10. Kaijura only: 9.5. Hosoe only: 7/10.