I would imagine the difference is the same as the difference between the zx6r and the zzr 600. Just a more touring oriented version of the same bike, without being a true touring bike. I'm torn between a zx12r and a zrx1100-1200r myself for my "I need this thing to be ridiculously fast" toy. Can't do it to the Z, I'm already in the process of turning it into the ultimate street fighter. I'll post a build thread by feb or march.
I've heard the zx12r is a great bike, just below the busa with better handling but a little less power and the only knocks I've heard is that there is a part of the wiring that always gums up with oil, there's a minor lighting problem and the throttle is somewhat like a on/off switch. All of those things are easy fixes with a little work and a pcIII I would think.
From what I've read, turbos are pretty easy to put on the zrxs', so that might be the deciding factor for me.