I agree that working out the file system would help some stuff... but then too, that's only assuming you want to use the hdd for the games that support it, too. If you only want to use it for homebrew, then it doesn't matter, as long as you are consistent.
So you're interested in making a MIPS port of Linux hey? Good luck with making all the drivers for it Nah seriously, that would be ideal. To have drivers for every device on the PS2. That would help development immensly. But there is a helluva lot of work involved in that.