When I purchased my FZ6 in August of 2008 I did about a month's of research before stepping foot on the showroom floor.
I was coming from a Yamaha XT225 dual sport, and a Honda CL200 before that. I had roughly 6,000 miles of road experience between the two bikes, although I had no experience with the larger road going motorcycles.
At the time, a 500-600 cc bike was the next logical step between the 200 cc class and the 1000 cc machines. I never even considered anything over 650 cc's which put the FZ1 out of the running. My short list included the following bikes: FZ6, Ninja 650R, Ninja 500, and the GSXR650F.
I found the FZ6 to have the best build quality, most refined motor, and included features for the price. I love the sound of an Inline 4 motor screaming to the redline which pretty much ruled out the parallel twin Ninja bikes. I liked the undertail exhaust of the FZ6, fuel injection and ride quality of the FZ6 which explains why I bought it instead of the GSXR650F.
Now that I've owned my 2008 FZ6 for a little over a year, and 7,000 miles of riding, I can honestly say that I'm thrilled with my purchase. I've considered stepping up the FZ1, but I'm having too much fun on the FZ6. It's cheap to insure, gets good fuel mileage (40-42 mpg) and is more than fast enough for me. The FZ1 gets worse fuel economy, has a smaller tank, is more costly to insure, has a higher purchase price, and will undoubtedly be harder on tires.
Bottom line, I'm going to hang onto my FZ6 for a good long time! I'm probably going to add an aftermarket exhaust system next year and maybe even a HID/ projector to improve the lighting.