Having ridden both the FZ6 and FZ6R I can say without a doubt in my opinion the FZ6R is a much superior motorcycle for the demographic it's aimed at. That is a budget street oriented street motorcycle. I've also noticed the legion of people who seem to automatically assume the FZ6 is the better motorcycle based on the stat sheet (FZ6 has more horsepower! FZ6 has aluminum frame! etc) and who constantly put down the FZ6R as a crap bike but in reality, the FZ6R is way more refined. It has a better clutch, a smoother engine, a more exploitable powerband, the steel frame actually improves balance and mass centralization - and it just overall rides and feels like a much better motorcycle. The best way I can describe it is it feels as if the FZ6 was a bike developed in the late 90s, with all the quirks those bikes had. The FZ6R feels like a modern motorcycle up to today's higher standards.
Still the FZ6 is a great bike, and with used prices so low it is a pretty screaming deal used especially compared to a new FZ6R which is a bit expensive - I just think the owners should stop bashing the new bike so much especially considering from what I can tell most haven't even ridden it.