2. HDD flexibility. I prefer using NTFS for my Wii games partition; ISOs do not need to be split (like with FAT32). If I ever have to replace my HDD, the process would be simpler and quicker. I can also just take my Wii USB drive out, plug it into my Windows PC, and game from there with Dolphin if I wanted to. I actually have two Wii's -- one for my wife and I and the other for the kids. We can swap drives if we want; sometimes the kids will want to play with the one that has saves from when the whole family joined together, but in their own space. Or they may even take the drive over to their cousins' house. (Wii U drives are tied to the console).
Just so you know, Dolphin supports loading wbfs and there are less than 5% of the games need to be splitted in wbfs format (and splitting is no big deal, you can use WBM to manage those automatically). wbfs format also saves a lot of hdd space (in fact most Wii games from the internet are in wbfs format already). It is actually much more convenient to have everything (Wii related) stored in one big FAT32 partition unless you want to store big PC/Mac files on the same drive.