It's not a mistake.If you choose for ntfs when you started with your harddisk, try to admit you made a mistake, repartition it and get over it.
It will give you the opportunity to remove the stuff you never use as well, and all files will be nicely defragmented.
Other USB loaders and WiiMC all support NTFS, and many users already have a substantial amount of data already stored on thousands of NTFS drives. Personally, I don't have the space on my PC to copy over all of the data which is presently on my 1 TB external drive. Up until now, no modern release of a USB loader has required users to revert back to FAT32. Why is the user supposedly at fault for having adopted standards which have been well supported by other major Wii applications for several years now?
Rather, IMO, what is a mistake is not to support a file system which is currently used by a significant percentage of one's potential user base. If/when it gets released, Devolution will be the first major USB loader from the past several years which does not support NTFS (DM will not either, but that appears to be more of a real technical limitation than an ideological issue).