I am not an R rider, but I did own the FZ6 for a while. It's a great bike, but the seat was BAD, at least for me. Corbin cured it. Other than that, I really had no issues with it. The only reason I got rid of it was because I was wanting a BMW (mistake) and SWMBO couldn't understand the need for more than one motorcycle.
When Yamaha came out with the R, the writing was on the wall for the FZ6. It was going away. I was disappointed, and like many in the FZ6 crowd, immediately wrote the R off as "crappy".
I was wrong. I have come to see that the R is a very nice bike in it's own right. It gets great reviews, and is a better competitor against the Ninja 650 and the GSX650 than the FZ6 was. Not because it's a better bike than the FZ6, but because it is a better bike than either of those and allows Yamaha some room to compete on price. Yamaha came out with the FZ8, and the way I see things, that is the replacement for the FZ6.
I think the R is a great looking bike, and I like the under belly muffler much better than the under seat mufflers on the FZ6. It runs smaller (less expensive) tires than the FZ6, and I assume insurance would be a bit less, but who knows?