Sorry for the long wait - I was at a conference.
The FZ6S2 is a great bike as can be seen by its sales success in Europe over the last few years. It doesn't vibrate much by my judgment. I agree that the engine is somewhat high strung and develops most of its superior power up high in the rpm. Around town it is plenty enough for me. It is a good looking bike and to me looks do matter.
It has a center stand standard, aluminum frame (so it is lighter), superb brakes and overall excellent transmission. The 1-2 gear change could definitely be better. I also encourage a test ride. I think that it is slightly sportier than the GSX650F even though the riding position is somewhat upright and similar to the GSX650F (I recently confirmed this at the NYC motorcycle show - They had a great orange GSX650F) . For my type of riding (more sedate, never above 7k rpm) I suspect that the GSX motor would be much better, but I never got to ride it. Under seat exhaust are very nice looking, but if you are stuck in traffic and it is more than 90 degrees outside they act as a bun warmer.
I really like Yamaha's workmanship - better than the previous Kawasaki I owned.
Overall, it is a very good bike. I really wanted to compare it to the GSX, but couldn't find a test ride. It is good enough that I am not going to sell it for a number of years.
Oh, and the seat is good for my bun. I do know that for '09 the comfort seat is standard now. The FZ6R is supposed to compete with the GSX more directly now.
