I've never liked MTP, so I don't use it. I use ADB instead.
I have a Windows command line utility adbsync.exe which can sync directories over ADB.
If you have multiple directories to sync you can put it all in a batch file or a makefile.
For example:
This backs up the latest photos, copies over new books and does a bunch of other things.
Likewise I have the equivalent for my Go6.
Of course you could make this an alias or a desktop link or a hotkey.