Knowing that you've had both, aside from the obvious, what are the standout differences? Wind protection? Day to day use? I'll likely log a ton of commuting miles and I'd like to be comfortable.
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Biggest difference aside from the obvious power difference is the seating position. FZ1 feels a lot more compact, your knees are bent more and you sit more upright. The FZ6 is a lot more balanced, your feet are lower, you have more space to the bars. The 6 is a much more comfortable bike for long distances. With no other interface mods than a Corbin seat and Throttlemeister I could do 1000-1200 days repeatedly with little discomfort, FZ1 not so much. The 1 is still a good bike for long distances, but the 6 is significantly better. Supposedly the 1gen FZ1 is a much better tourer, but I just couldn't go back to carbs.
Next biggest thing is fuel consumption/capacity. FZ6 has 19L gas tank, FZ1 has 18L gas tank. FZ6 fuel economy was about 50mpg, with minor 5mpg fluctuation depending on what I was doing. On the FZ1, I've seen anywhere from 25mpg to 40mpg depending on how I ride, averaging about 35mpg. That translates to a steady 360km range to dead empty on the 6, to an average range of 260km to dead empty on the 1. The 6 engine was stock aside from a slipon, where the 1 has a PC3 and full Yosh exhaust. Probably doesn't help fuel economy, but my numbers are similar to what most others are seeing.
Wind protection is about the same, maintenance is the same, tires are more expensive and more frequent on the 1 with the 190 rear and more power. Luggage options are the same. I've had full Givi hard bags on both. Handling feel is similar, but the suspension on the 6 is obviously inferior. Doesn't cost too much to fix, I had R6S forks on mine. Both have centre stands for easy maintenance on the go. FZ1 has awesome stator output if you're using heated gear
The FZ1 has more power, and is a lot of fun that way, but you can't really use it to it's full potential around town without killing yourself or getting in trouble. The 6 is a lot more usable at legal speeds, and in that regard, more fun.
Edit: the underseat exhaust on the 6 looks absolutely bitchen, and actually runs/feels cooler in traffic compared to the 1