Very hard to make a comparison on this since they are two completly different machines. This is almost like someone trying to compare a buell to a harley, different machines.
I have put some miles on a friend of mine's 600r and the only thing similar about these bikes is they are motorcycles produced by yamaha. The 600r is carburated, has a more aggressive riding position, has analog guages, its wider and feels heavier. Both of these bikes are more capable than any street rider would need and very few people can even get close to riding either one of these to their full potential.
If all you are looking for is the best all around bike i would go for the fz just because it uses up to date technology and it doesnt have the tranny problems the 600r has. The 600r has been unchanged since 97 if that helps you out any.
Also we have taken our bikes to the drag strip and i beat him by only 3 tenths of a second. So if you want speed they are equal in comparison. Just remember one good rule, it all depends on the rider.
