I also traded my 2015 FZ09 in for a 2016 GSX-S1000 and it was a decision well made. Although the triple of the FZ09 is full of torque with a fun power band, it was hard not not to over look it faults, those of which I have not found with my GSX-S1000. First of all, the chassis and suspension of the FZ09 is downright dangerous, especially for canyon riding. The super soft suspension and pogostick-like chassis stand the bike up in corners and create a hurky-jerky ride that coupled with a twitchy throttle response can put you on the ground if you're not careful. The overall chassis and suspension package of the GSX-S1000 is much more put together and stable, the throttle response is not nearly as twitchy, and the engine absolutely PULLS. In addition, coming from a dirt bike background, I liked the up-right position of the FZ09, but it became very tiring while commuting a good 45 mins to and from work everyday on the freeway. The GSX-S1000 tucks the rider in a bit more, and although its is still fairly up-right, you don't get nearly as tired. Also, the transmission on my FZ09 was very clunky. It would often get stuck in neutral when downshifting quickly and was very clunky when shifting from neutral to first gear. I have put 1500 miles on my GSX-S1000 with nothing but a buttery smooth transmission. Lastly, I felt that my FZ09 was very buzzy. There was a lot of vibration at the bars and pegs when cruising at freeway speeds. My GSX-S1000 is super smooth and anything but buzzy at the same speeds.
Trading the FZ09 for the GSX-S1000 was definitely an upgrade and it's a decision I'm happy that I made!