FAT doesn't really have any negatives, other than having to split files larger than 4gb. The downsides of WBFS far outweigh those of FAT32.
You get "nice managers" with all filesystems, but with FAT (and NTFS) you aren't stuck using them. WBFS is a relic from the past. If you are still in the past and use it & it works for you - great! But for anyone just starting out it makes far more sense to use FAT. We wouldn't recommend people install the very first cIOS, and nor should we recommend people use a FS that has been superseded.
The .wbfs file was also made for wii games.
In addition to all that using FAT32 opens up the HDD for use with homebrew. I have several gigs worth of videos and roms stored on the HDD that I watch/play through homebrew software.
Sure you could partition the drive to WBFS/FAT32 but why go through the trouble when formatting the entire drive to FAT32 works just as well? I'm not saying FAT32 is the best file system out there but atm it is the best option for the Wii. I'd personally prefer ext3 but no one has seen a need to support it yet.
QUOTEAnd if nobody released a CIOS for fat32 or NTFS you'd still be using it.