There's a plenty of open source filesystems, many of them really great, ranging from simplest to most sophisticated. There's one big pain about them though. It seems that none of them is supported in Windows

You can make any filesystem you want (I recall some of mine from the pre-PC days when a winchester disk occupied a 19" rack) but if you stick with the "PC standard" all utilities will/should work. If you make your own you will eventually have to write a disk defragmenter and who knows what else. So, why not just stick with the standard.

I will, at any time, ignore a standard if there is a pressing reason, but ignoring a standard just to try something else does not make sense to me.

So, how hard would it be to make '51 behave i.e. as an USB CD writer
If you choose a USB hard disk format, not very hard, Cypress have a free reference design with all hardware and software (in source) that match a $5 chip of theirs. You will have to fill out a form to get it.

Erik