Although the MFT may not be externally fragmented, and shouldn't be on a proper installation of the OS, it can become badly fragmented internally. Small files are written entirely within the MFT. So, if the system has a lot of small files being written to and erased from an NTFS partition, then the MFT is very likely to become badly fragmented internally. The fix is a boot-time defragger that utilizes the appropriate APIs for defragging the MFT.
BTW, though it's based upon the same basic idea as the in-built defragger, the commercially available Diskeeper (Executive Software) is much faster at defragging than the basic defragger -- at least on all of the systems on which I've seen both defraggers used.
- Collin