The knobs for shutter speed and exposure compensation on the 645N are big improvement over the 645 body's goofy up/down buttons. With this change and Matrix Metering that you don't have to try to out-guess, the 645N becomes about as intuitive as a camera can be, at least I find it so.
I'm not exactly sure what the 645N II does so much better than 645N as to justify two to three times greater price on eBay. Admittedly, they do look a little nicer with the matte finish and the different texture to the naugahyde. There was also more customization available to the data imprinting, though I don't believe that these settings are user-changeable (they're service-center changeable, but I haven't been able to determine exactly what they are, and some time ago, Pentax dropped customization as a service for the 645N, at least). Jury is out on the need for mirror lock-up on the NII. Now, on my Pentax LX the mirror-up function is very useable while doing 1/3 stop auto-exposure bracketing since the metering is done continuously off the film plane with the meter cell inside the mirror box on that particular camera (not just the flash sensor in the mirror box). While the viewfinder is blacked out with MLU the metering is still happening in real-time. On other cameras with the metering in the prism (645, 645N, & 645NII all, as far as I know), MLU can be inconvenient to use as you have to manually meter or exposure-lock prior to flipping the mirror up and making the exposure.
Another minor difference between the 645N & NII is that they use different electric cable releases-- the NII one being rarer and much more expensive. What I have found, though, is that the 645N is strangely sensitive to latching the metering in the half-depress "on" conditon instead of it cycling off and going to sleep after 30 seconds after the button is released or after an exposure, whenever I have an extension cable spliced into the stock cable, or whenever the camera is wired into an a PIR trigger for my night-time wildlife remotes. Perhaps someone will chime in to tell me that Pentax cured this on the NII.