I particularly thought that the original Shadow Hearts was the best as it was the most distinctive of the three. Since I've never played a Shadow Hearts game before, I'm not sure how much I can say the music complements the game. From what I've heard outside of the game, SH1's music impressed me most with it's heavy staccato-sampling, triphop-funk-jazz found on most pieces (like the world map tracks), and the downright eerie "But Dad Dead Bed" (I have yet to hear something so emotional in such a small piece) and other sour-sounding/downtrodden music that have not been mimicked in SH2 or SH3.
Personally, I find Hirota's newer/recent stuff to sound too much alike with too much world music (including the excessive chanting and string instruments) and way too much staccato sampling and less of the isolated-feeling jazzy stuff which made the first soundtrack so special. I won't go along and poo-poo any of Hirota's newer stuff even if I'm not very fond of it as he's capable of further brilliance (like "The Fate" from 2) but I think Mitsuda stole some of Hirota's steam on SH2 especially with "Twilight Street".
When I heard Shadow Hearts 3, I heard more of 2's style, and even more of a deviation from 1 which shut me off to it and the Arrange album.
Oh yeah and I think Shadow Hearts probably has some of the weirdest/coolest track names I've ever heard.