About the most negative thing I read on the FZ1 was last years naked sport comparo in Rider where their test model "burned oil" as they put it.
Other than that, their comments went like this:
"...the clear winner was the Yamaha FZ1. With its cushy seat and reasonable seating position it was the most comfortable, extremely stable in turns, offered the best suspension and absolute pin-your-eyeballs-to-your-face-shield brakes. Now factor in that it has the highest horsepower, delivers decent fuel economy and is priced at $8,599, and what's there to compain about?"
So far the reviews I've seen on the '06 reflect a similar "negativity"...boy am I glad I snapped up my new '05 model discounted to $7599! So far I must concur with the review--it is all those things except one...mine, being properly broken in doesn't burn oil.
Now, a REAL negative does exist...the pre-'06 carb models are rather cold blooded, and a bit finicky about starting until one figures out to crack the throttle a touch, then it starts superbly. This isn't a major issue, and doesn't justify the fix which requires readjusting the float-height...something to do when one gets around to a little performance carb tuning.