Now that being out of the way, my last bike was a YZF600r thundercat.
I loved that bike and put about 32000 miles on it in 3 years. It was refered to by my wife and I as the rolling couch, it was extremely capable, comfortable and had plenty of power (i thought... he he he). the forks were "better" in the sense that they were fully adjustable, but no matter how much tweaking i did they still needed internal parts replaced for anyone over 190lbs.
I was extremely worried about switching to the FZ from the yzf, but it was time to get some newer technology and i loved the 2007 re-design, so i decided to take the plundge and trade it in for a brandy new fz. the geometry of the bike is almost identical, the seating position is actually a bit more upright than even the thundercat, so i feel it is more comfortable. the Power is much smoother and being fuel injected makes the throttle response much quicker. The FZ is suprisingly even better (according to my wife) for 2 - up riding (and she has actually fallen asleep on the YZF). The FZ is also a lot lighter which accentuates the 13 extra horsepower. Also the New gauge cluster is way easier to read than the YZF's all analogue cluster.
The downfalls are this, even though the wind protection on the FZ is great and can probably be fixed with a new windscreen, the YZF did have better wind protection.
I am sure that with either bike you would be fine, but Personally i would not go back to the YZF if i had the chance, but i do want to say again, I loved that bike!