Jim Zemlin wrote in his response to the settlement:
The technology at the heart of this settlement is the FAT filesystem. As acknowledged by Microsoft in the press release, this file system is easily replaced with multiple technology alternatives.
This was also quoted again by Groklaw in their article. But is this actually true? The major benefit that FAT brings that other file systems do not is its ubiquity. It's supported without the need to install third party code on Windows, MacOSX and Linux along with countless other devices and operating systems. No other single file system has such cross platform support.
If you're developing an embedded device with internal storage (e.g. a PTP camera or MTP media player with built-in flash memory) then you can get away with using whichever file system you like (and I've worked on products which used ext2 and reiserfs in this situation.) Unfortunately as soon as you start using removable storage or need to make your built-in storage available as a block device over USB mass storage class or similar then you need to be interoperable. Being interoperable means using FAT or if you are very lucky and you have a knowledgeable user base a file system such as ext3 which can be supported on Windows and MacOSX with a little work.
FAT's simplicity makes it even more useful for interoperability. It's lack of support for ownership and ACLs means that you can just plug a USB key in and start reading and writing to it immediately. A more advanced file system such as ext3 just gets in the way if your UID doesn't match between different machines or you give the key to someone else. This problem is less of a worry for an embedded device which may just run as root anyway or can be hacked to work around this. On the desktop there may be a case here for supporting mounts in a special “ignore permissions” or “everybody squash” mode to solve this problem.
This topic has become important to be because recently I've been looking into alternatives to FAT for a completely different reason: resilience. FAT, and in particular FAT as implemented on Linux, is highly prone to corruption if someone pulls the USB key or the power cable. Other file systems such as ext3 are much more capable of dealing with this.