I had wondered about the filing system actually. The current one, for all that it may have been a nice system when it came out, is a pain for compatability.
It may even be good for riscos to be forced onto a FAT file system. I'm vaguely aware that its flawed and outdated, but also that it is, as you say, the fs of choice for flash memory where the problems with it account for little.
Obviously this would also be a lot of work, but were it to happen I feel it would be removing an important obstacle to file compatability (This is based off limited knowledge of the issue though, so may be of no consequence).