Personally I like the PS2 version better. Brushing is easy in the WII version but battles are a pain when it comes to swinging with the remote. This makes battling ten times slower than in the PS2 version. You have to push the stick of the nunchuk really hard to make Ammy run or else she'll constantly walk instead. The voices of the characters are a lot softer in the WII version and if you don't adapt the music to a lower stand you hardly hear the crazy mumbling sounds. Plus I like the lighter paper rice GFX better in the PS2 version, I find them kind of blurry in the WII version and too dark. Its nice there's a skip option, but why the heck do you want to skip a wonderful cutscene with the crazy Issun?
The game is a total must have if you have never played it before but if you already own the PS2 version, I'd say stick with that, IMO.