I ridden an FJR and owned two Connies '13 and now a 12. I looked at the FJR pretty hard before buying the first Connie. I like the looks and the electronics package that it offers in the newest/newer models, however, the cost set me back a bit. What did it for me was riding my Son's '15 C14 in the Eddie Lawson Green which is really beautiful, but not my color choice. I am 5'-9", 150 lbs dry. The C14 fit my criteria for a large but not huge bike, and I assume the FJR would have done so just as well. My requirements were, in no particular order;
1) more than fast enough to get into and out of trouble, with a solid motor history, both offer this. I don't care much which bike is faster because it is the rider not the bike that define this metric.
2) comfortable on longer rides (perhaps with seat mods), I never ride two up so this did not register on my list.
3) enough aftermarket farkles and such to keep my bank account drained if I wanted to indulge, I cannot recall how many farkles I have indulged in...
4) solid footprint on the pavement and handling that works well, meaning not twitchy, not lethargic. The C14 works great with Michelin Road 4GTs or Road 5s.
5) reasonable gas mileage, but who buys these machines for efficiency beyond a certain point? I tend to average 40-41 in town and 46 on the open road at 80MPH, 90 seems to be the sweet spot for wind comfort, smoothness and all around high speed, low drag straight highway riding,
6) good carrying capacity and storage, I like to carry enough e-supplies in case I or another rider may need something, the Connie has a 22 lb. per saddle bag limit, about 12 lbs. in the top case.
7) a bike I could pick up when, not if I tip it over which I did 5 minutes after I left the dealer with my '13 dam-it...and yes I can pick it up.
good coverage from the fairing while not looking like I have a billboard in front of me and aftermarket screens to fit my size, with or course electrical lift,
a large and supportive riders group which both platforms offer in abundance.
I have farkled both Connies, starting with flashing the ECU. On the C14 I noted that slow speed maneuvering like in parking lots it felt a bit jerky and was not confidence inspiring; the flash fixed that, removed the top speed limit (now 173) increased HP and torque by about 5HP and 8lbs/ft. respectively and in general enhances the performance through the RPM range.
Went to a Cee Bailey screen which I found works best for me, unfortunately they stopped making them- another curse word.
Modified the seat to resemble the Kawasaki touring seat which lowers the seat height about 1.5" without it diminishing comfort,
added Denali DM "conspicuity" lights in front, and HIDs to replace the regular headlights, and added switchbacks for front and back, all of which were great upgrades, and on and on with other stuff to make it my own bike and am very, very happy with it.
Many C14 drivers would like to see Kawasaki update the platform with cruise; I went with a Kaoko throttle lock and have been very satisfied with it. Less to mess with and fail on the road. Personally, I would like to see a modernized instrument package with a TFT like display on the FJR and the new H2 platform. Kawasaki tried (feebly) to market the H2 SE as the new Connie but we know better. I went to a Delkevic slip on carbon fiber exhaust which is so much lighter than the stock exhaust, and sounds nice to me. I prefer quiet bikes which can sound good when opened up, the Delk does this well. Some drivers spend $2K to upgrade the suspension with Traxxion Dynamics forks and a Penske shock but I can't see the cost benefit given my weight and riding style, which is smooth rapid progress through the city, we do not have lane splitting in WA but can ride any HOV lanes. If anyone reading this has been to Lolo Pass through Montana and knows that road, the Connie carved it up very nicely, easily holding the lines at 80-90 plus without any issues. If you have not been there, it is 99 miles of high speed sweepers going up and over the pass at ~5000 ft. I rode the '12 from SEA to LA and back last summer with no issues, 100+ degree heat, and down to the high 20s over the passes with no issues. The faring keeps me dry and warm, I note that when it is raining and I don't have wet weather gear on, only my knees get a bit wet, everything else stays dry behind the fairing and screen unless of course I am stopped at a light. Heated grips are the bomb, how did we live with out them?
I don't think you can go wrong with either bike. Both bikes IMO have weathered the years with good forward styling, standing the test of time. My buddy is looking at an '09 FJR this AM, so it is on my mind. He is about 5'-7" and is concerned about foot placement on pavement so we will see how it fits him. The FJR looks a lot narrower than the C14 and is actually a bit longer so Yamaha did a good job of making it look smaller somehow.
That's it for my longish response to the question, hope it helps. BTW my C14 is called Fat Ninja.