Sorry, I missed your post.
Well, the main difference for me is 12 is much more stable than 11. PP is very idiosyncratic and user's experiences vary tremendously depending upon the OS and software environment in which it runs. For me, 10 was good though some bugs were there; 11 gave me a lot of headaches, some of which I found workarounds for, others which never resolved.
One bug improvement is annotations which in 11 (10 also?) would not print out properly.
The paperport users group (yahoo) members state that a difference is that PP12 creates searchable PDFs without the need for Omnipage.
It's UI has changed: instead of the menus, it uses Word2007-style ribbon up top, with quick access toolbar for commonly desired functions. Some folks don't like that.
There are now two separate programs outside of the main paperport desktop: (1) imageview, which is like the old pageviewer, and (2) pdfviewer, which is an alternative to Acrobat and has search function for searchable pdfs.
All-in-all, if you don't use searchable pdfs and if 10 or 11 is stable and error-free enough for you, then you don't need to bother with PP12; I think that is the general consensus of many long time paperport users (based upon user-group discussion).
edit: they also added "themes". You can choose from a variety of desktop color combinations.