The wbfs vs. fat question has been addressed MANY times, in this thread and elsewhere. If the speed issues have been resolved, which appears to be the case, there really is no reason not to use FAT32, unless you just can't stand the idea of having split files for the games over 4GB, or the use of titleid's as filenames necessitating an additional .txt file for easy identification. The advantages of FAT32 are the ability to use any of the disk tools such as defrag, repartitioning, etc. And if you like to use the homebrew ISO forwarders, such as for Triiforce NAND loading from within the USB loader, you can put those onto your drive with ftpii so you don't have to move the drive around. Of course there's nothing stopping you from doing it with larger ISO's as well if you have the time.