Licensing costs may be a part of it EDIT - See below. "LFN" (long file names) is the abstraction layer _on top_ of FAT which gives you > 8.3 file names, and it is a patented Microsoft implementation. That said LFN works on FAT 12/16/32.
"A more advanced filesystem" would be FAT 32 which most all new cameras are using - 4GB is the formatted drive size limit with FAT 16 if you want to get tricky, 2 GB is the default max size.
Canon cheaped out on the 300 and 350 (IIRC) lines and could only format a card FAT 16, but would gladly read FAT32 cards formatted elsewhere.
EDIT - the more I read the more it appears LFN is the most expensive license (or at least the only actively enforced license). - I guess that answers that.