Couldn't you just put a new file system on MBR and still make it work?Does the firmware need flashing?Why is FAT16/32 is so popular?
closed as not a real question by BloodPhilia, haimg, Simon Sheehan, studiohack♦ Dec 30 '11 at 21:37
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The MBR is essentially a "boot-sector" that describes the partitions of the drive, and where the location of the first piece of machine code that the computer can use on the drive.
FAT16 & FAT32 on the other hand are the file systems that the partitions themselves can use.
The reason why FAT16 & FAT32 are commonly found in devices is because they are very well supported by most (if not all) operating systems so compatibility is rarely a problem. Even if the device does not use a conventional operating system FAT32 implementations can be found for most embedded devices or, if not available, is simple and well defined enough that implementation is easy.
Any maker of embedded devices can use whatever file system they like, but using FAT32 generally means that if they are to be connected to a computer then all it needs to do is expose it's flash memory as a USB mass storage device (also a well defined standard) and the computer will do the rest. If they use a non-standard file system then they will have to write an intermediate driver, either on the computer or on the device itself which is a lot more work than just using standardised formats.
Basically it boils down to effort. FAT32 is easy, reliable, and suitable for almost all embedded systems that do not require a high level of security. Other filesystems may have benefits but they lack the "universal" support.