I'm using MacFuse 2.1.5 with no problems so far. The Reinstall Parallels Tools menu item worked for me. Autoinstall should work fine too.
The MacFUSE file system mismatch error occurs when you try to mount a volume that uses a MacFUSE file system when the currently installed version of MacFUSE is different than that used by already mounted volumes. Installing a new version of MacFUSE does not stop currently mounted volumes from using the previously installed version of MacFUSE.
For example, I was using MacFUSE 2.0.3 beta. I updated to MacFUSE 2.1.5 beta using the MacFUSE Preferences Panel which automatically removes the files of the older version first. I unmounted my Ubuntu partition which is using the fuse-ext2 file system. When I try to remount my Ubuntu partition with Disk Utility, I get the MacFUSE file system mismatch error because I still have other volumes mounted that were using the NTFS-3g file system with the old version of MacFUSE.
The MacFUSE file system mismatch error tells you to unmount all volumes that are using MacFUSE before mounting a volume with the new MacFUSE. It also says that restarting is another way to use the new version. After I unmounted my ntfs-3g volumes, I could then remount them and Ubuntu so that they are all using MacFUSE 2.1.5 now.
Parallels Desktop also uses MacFUSE to mount the Windows disks of your running VM's on the Mac. Most volumes that are using MacFUSE will state that in their Get Info window where they state their Format.
The best way to update or remove MacFUSE is to use the MacFUSE Preferences Panel. I think the Remove button uses the following script:
/Library/Filesystems/fusefs.fs/Support/uninstall-macfuse-core.sh
There's a discussion of removing MacFUSE at:
http://code.google.com/p/macfuse/issues/detail?id=36
There's a discussion of an experimental 2.1.7 version at:
http://code.google.com/p/macfuse/issues/detail?id=346
All issues and updates are listed at:
http://code.google.com/p/macfuse/updates/list