I traded my FZ07 in on an R3. I only put 1900 miles on the FZ07. It was a very good bike with lots of torque and of course does highway speeds very well. Only thing I didn't like about mine was the seat ht. and weight. No, 398 lbs. isn't heavy, but along with the taller seat, I would get cramps in my hips once I stopped and put my feet down at traffic lights. 30 lbs. makes a huge difference along with the lower seat of the R3. The other reason I traded the FZ07 in was that I have another red naked bike...the CB300F, so I wanted another color. I also have a Zero S with loads of torque so I can get my torque fix whenever I want.
To me, the R3 is an outstanding highway commuter. That's what it does best. If you do a lot of highway riding, it would be an excellent choice. Better than the CBR300R or the Ninja 300? Maybe not. I probably wouldn't trade in a CBR250R for an R3, but the R3 will be noticeably faster and have better acceleration from 40 mph on up. The R3 hugs the road at 85 mph very well. I took mine up to 95 mph briefly and it was still well-planted and purring. It got there quickly too. My preference for a city bike is the CB300F with the same engine as the CBR300R, but naked, lighter, and with a more up-right riding position. Any of these 250/300 bikes will work for both city, commuting by highway, or riding twisties. The 300s are faster and don't work as hard as the 250s at 80 mph, but whether that's worth going from a 250 to a 300 is hard to say. My 2012 Ninja 250r wasn't very well planted on the highway going 80 mph and while it did that speed easily, the little engine seemed to be working pretty hard. The 300s have wider rear tires which might be part of the improvement with stability at higher speeds too.