The FJR1300 is Yamaha's competitor in the sport touring arena. They've tried to carve out their own niche by making the bike a little sportier than the others and calling it a "Supersport Touring" bike. It's a favorite with the long-distance riding community (the Iron Butt Association guys/gals) because it's comfortable for long rides, has lots of power, handles well, is faired, and has decent luggage. You can also modify the heck out of it. Here's a link to a picture:
FJR1300
The FJR corners better than the Rocket - it leans farther, and you can carry quite a bit more speed through the corners. It also has a higher top end; mine maxed out at 158mph indicated, which is typical. The Rocket will smoke the FJR off the line and will pull well out of the turns, but on a twisty road with riders of equal ability, the FJR wins. If I wanted to take a LONG trip (e.g. cross-country), I'd do it on the FJR. That's not to say you can't do it on the Rocket, but it would be less comfortable.
I had this same conversation on the FJR forum recently, and someone asked me to pick my favorite of the two. Sorry, can't do that - they're too different. I like them both!
My $0.02 worth.
RickL