I totally forgot to mention another change Yamaha made when it comes to cheapening the FJR on the gen3 machines that being building the front subframe out of brittle pot metal rather than welded steel tubing. So, don't drop your gen3 on its side else you might just crack the front subframe when the rear view mirrors hits the dirt and you get to have loads of fun changing out the subframe. Yamaha probably promoted this change as weight savings. Yeah right!
That is the ONLY thing I agree with you on about Gen 2 to Gen 3 getting worse. As far as I am concerned, the gauges on the Gen 2 are the worst. Hard to see, and move/vibrate with the windscreen if it is moving. Other negatives of Gen 2: '06 and '07 don't have the updated ABS brakes and had their own issues. Going back to the reduced effort clutch slave cylinder didn't happen until the '09 model. And then there is the wiring harness fiasco with the ground spiders. I am not positive on this, but I don't think that was fixed from the factory (not requiring the recall repair) until 2012. Also for me, after trying to live with the stock suspension on my Gen II, I HAD to upgrade forks and shock. Whereas my stock ES suspension on my '14 and '17 is great.
Don't get me wrong, I love my '09 FJR and have put 140k miles on it. But the Gen III+ offers a lot of refinement and AFAIAC, is a much better FJR. Now that being said, I still LOVE to ride my Gen I '04 FJR as it is less refined and a bit rougher around the edges and more FUN.