The trick is that the main processor of the PS2 is included in the PS3. Unfortunately, they're not including the chip that did the sound processing, so they have to write software to mimic its functions. And that software isn't 100% complete yet.
I'm not getting a PS3 (ever; I'm avoiding Sony products. Never got a PS2 either.), but I'm reasonably confident that Sony is working on this problem. However, they -never- got the sound quite right for PS1 games on the PS2, so I wouldn't expect perfection. [disagree? compare FFT music between the two systems. There's a difference]