I really liked how Shimomura handled the KHHD soundtrack. She simply improved the instrumentation and made small adjustments to bring out slightly more distinct musical flavor in some tracks. The music no longer sounds tone generated, but it still sounds like the same music. It's recognizable despite the huge jump in fidelity and the fact that no one complained that the original ost wasn't an option says a lot about how effective the remastering was. That she managed to do such an incredible job with it says a lot to me about her talent and professionalism. I absolutely can't wait for 2.5 to hear how she handles that one, considering the original ps2 instrumentation is extremely weak compared to the first game.
Hamauzu didn't improve the instrumentation, he changed the instruments completely. Many tracks don't even sound like the same songs, with layers of extra instruments and sounds thrown in, diluting it even more.
Honestly it's unforunate, but the fact that they needlessly tampered with the main character models and animations is a lot more egregious to me. Upping the resolution, touching up textures here and there, etc... that's one thing. But when you start altering geometry to change a characters appearance entirely for dubious reasons, then it's going too far. This isn't some low poly npc that never stood out due to the low resolution of the original game - these are the main characters, and everyone knows what they are supposed to look like.