Having played both, I can say that the PS2 version is definitely better, mostly because the controls seem like a better fit for the PS2 controller.
The Wii port just reeks of... well, Wii port. The controls are decent enough, but the whole control scheme just seems alienated and unnatural, despite what you'd think from motion and pointer controls. A game like Okami just seems to benefit from having a button-based controller in all areas. Even subtler things become an annoyance on the Wii. The camera is indeed a pain to move around on the Wii edition because of having to reach WAY up the controller to the control pad, and the Nunchuk's stupid-ass eight-direction notches it has on its control pad makes it harder to make subtle direction changes (though this is more of a fault of Nintendo, not the game).
The Wii's version loses out slightly in terms of graphics compared to the PS2 . The Wii version seems a bit darker in contrast compared to the original PS2 version, but you only really notice it when playing one right after the other. Also, oddly, it seems that some little graphical effects had to be sacrificed for the Wii port. The neat ink-and-parchment sort of sepia tone that the screen changes when operating the paintbrush is severely butchered. Sure, it's not that big of a deal, and still turns a bit sepia-ish on the Wii, but it's much more edgy and effective on the PS2 to be sure. Also, there's no bloom in the Wii version, which probably accounts for the lost brightness. On top of THAT, the Wii version chugs a bit more. I don't mind these cut graphical effects as much as I do the botched controls, but it irks me nonetheless, as the Wii has been proven time and time again to be quite the graphical powerhouse when put to the test, or at least compared to the PS2...
If you're really concerned about the graphics, here's a comparison video I found. It sort of sucks, but handy anyways.
EDIT: Ohh man, looks like a tie in the polls!!!!!!11