FAT32 can be used solely for the Wii as well...just because you CAN use it for other things doesn't mean you'll have to. I have a 640gb plug&play drive formatted to FAT32 w/32kb cluster size (this is needed to enable GameCube USB loading) and I only use it for my Wii...it only gets plugged into my computer if I need to do something with the files on the drive such as deleting or renaming a game file or backing up new games I've ripped.

But it is completely up to you, FAT32 is recommended but if you don't play GameCube games and find WBFS more convenient than more power to you