Are there any riders who have both that could compare performance,and handling?
You have found your man, and probably others here too. Here's my .02.
Bought a new FJ1200 in '89 and had it until two years ago. My web developer owns it now and I got to put 20 miles on it a few weeks ago. Disclaimer: My FJ1200 was modded with a Penske shock and an FZR1000 rear wheel (17 in rim) equiped with sporting rubber, so the handling was way better than a stock FJ1200.
Power: FJR1300 wins here. The two bikes are nearly the same weight, but the FJR has more torque and more HP. My FJ1200 with a jet kit did 118HP to the rear wheel with 78 ft. lbs. of torque. Most FJR1300's would pull 125HP or more and torque in the 90 ft. lb. range or more.
Smoothness: FJR1300 is WAY more smooth than the FJ1200. That thing seemed to rattle my colon when I rode it recently.
Wind protection: Again, the FJR
Handling: My modded FJ1200 handled pretty well. My FJR1300 has an Ohlins rear shock and I think handles better.
Comfort: The FJ1200 hurt me bad. That is why I quit riding it, but that is due to some proprietary physical problems that I have. The pegs were to high and too far forward for me. Also, the clutch pull killed my arthritus effected left thumb joint. I believe that the FJR1300 has the same clutch spring, but the clutch pull on the FJR1300 is much lighter. In all, the FJR1300 is way more comfortable, the only exception being some heat issues that are minor for me.
Touring amenities: I don't think I even need to comment here.
Economy: My FJ1200 average for all the years I owned it was 39.6. My '98 R1 has averaged 42.2 since new, and the FJR1300 has averaged 38.0 for less than eight months of ownership. No real trips yet to bring up that average.
Have I mentioned that I love the FJR??