Bike for bike I think the FZ1 is probabley a better bike, not to take away from the FZ6, I wouldn't trade mine for an FZ1.
FZ6:
Lighter
Better fuel economy
Bigger tank
Has 10mm narrower rear tire (quicker tip in, I guess)
generally much cheaper
FZ1:
40ish% more power
much better suspension (not that the FZ6's suspension is bad)
Still being made
10mm wider rear tire more grip
Personally I doubt that you would notice enough of a difference in the FZ6's weight and rear tire profile to offset the other differences between the two bikes.