If you simply alter the way the SWIs work it would certainly break almost every RISC OS app out there. There's on the other hand hardly anything that says that a new format with new SWIs to access it couldn't be created - translating the old ones automatically when applied to new format filesystems (you are all using SWIs to communicate with data storage aren't you?)
Moving to a new system would also allow for a different way to apply types to files by using name extensions, thereby moving towards what the rest of the world is doing. After all, easier communication with other platforms is what most seem to see as the be all and end all of computing of the future and certainly will have a big impact on wether RISC OS survives in the long run or not. Certainly the ability to read the files themselves are a bigger issue but having to filetype them and rename to move them back and forth are a huge irritation factor that most aren't really interested in enduring, just like AJW above.