Somewhere in the first sector (aligned to a 64 bit boundary), there would be a small structure that just contains a unique signature (not ASCII but some random value; 64 bits seems like more than enough as opposed to a GUID), and a pointer to the "FS info block". Leaving all remaining space in the sector available for boot code or possibly another "overlayed" filesystem.
That info block in turn would point to the MFT entry for the stage 2 boot code. An MFT entry would contain at a minimum an easy to locate list of (start sector,count) extents. Maybe there could be a flag that tells the OS that a certain file should never be fragmented?
File names would be entirely optional and for human consumption; for direct links within a filesystem, sector numbers would be used, and some kind of unique numeric identifier for anything "higher-level".
I'm genuinely wondering if some expert here sees any problem with this scheme, other than it not conforming to how mainstream OSes do things?