Carl,
I've included a link to the product bulletin on the Mitutoyo website. As it appears to me, level one is basically the inspection side of the application, level 2 adds the ability to import and program from CAD, and level 3 is for surface analysis, best fitting, section scanning and comparison, etc. My opinion from reading and looking at the pictures is level 1 is 6000 on steroids. It is a more step-by-step graphical environment with some very cool additions like a tapped hole inspection routine. Check it out:
http://www.mitutoyo.com/pdf/1701.pdf
Regards,
Terry W. Prather