At first I would say "there is no comparison" but there is some comparison.
They are totally different of course, and the FZ1 compliments the Bonnie well in that it reminds you what the Bonnie is NOT about. The Bonnie is great for around town, tight backroads, 2 lane highways, etc. The Bonnie is still fun for exactly what we already knew it was fun for. The Bonnie is still cooler too. I get a lot of thumbs up on the Bonnie, I get some dirty looks on the FZ1.
The FZ1 is a total fucking rocketship, the suspension is super smooth over even the roughest roads, and the brakes are scary powerful. It's a little bit of a handful in the city (hell anywhere the speed limit is under 70mph) because it just wants to fly and it's really tough holding it back. It just revs so fast and will accelerate to illegal speeds in half a twist of the wrist. The FZ1 is a bigger bike too. It's taller, wider, heavier, etc so tight maneuvers like in parking lots, on sidewalks, etc are a little more difficult than with the Bonnie, but still not bad. It is a pretty light bike itself, just a little bigger than the Bonnie.
Where the FZ1 really shines is outside the city limits. Open roads, whether 2 lane blacktop or multi-lane super slab, instant and vicious acceleration is just a wrist movement away. Wanna pass 6 cars? Drop down a gear and hit warp speed. Wanna go from 70-140mph in about 3/4 of a second? No problem. It's also very comfortable and smooth. Cruising at 70-80-90mph the FZ1 isn't even breaking a sweat. It also has about a gallon more fuel capacity so the range is better. The FZ1 is a MUCH better distance machine than the Bonnie.