My first FJR was a 2006 that I bought used in 2011 with 9200 miles on it. It was a great bike, the prettiest of all FJRs with the Cobalt Blue paint and silver wheels. I hate black wheels on a motorcycle. It didn't have heated grips, so I added the OEM plug-n-play grip kit. The only downside to the '06 was the fuel injection mapping. It sucked, with an on-off throttle response that killed my confidence during aggressive cornering. I installed the G2 throttle cam, which was a slight improvement. Then I installed a Power Commander with the Fuel Moto "smoothness" map. That mod helped quite a bit and made the bike much easier to handle, but it did slightly increase fuel consumption. Not cool, because I like to get as much range from a tank as I can when out in remote areas.
That bike was totaled in a crash in late 2014. Once I got the check from the other guys insurance company, I was shopping for a new FJR. I didn't want a 2013 or 2014 model because they have black wheels. The only logical choice was a new leftover 2012 model...Cobalt Blue paint, silver wheels. I found a dealer in Clearwater FL that had three leftover 2012s in stock...a 50-state unit and two 49-state units. My buddy and I bought the two 49-staters over the phone. I flew to Florida two weeks later to take delivery and ride it back to California. It currently has 75000 miles on it, and I have no intention of ever selling it.
The only visible ways to tell an '06 from a '12 is the FJR logo-decal on the side fairings on the '06, and the '06 has silver trim around the speedo/tach cluster. On the '12 it's black. The '12 came with standard heated grips. And the fuel injection mapping...it's a night and day difference. The '12 is so much easier to ride aggressively, and you don't take a mileage hit in the process. Sure, it doesn't have cruise control and all the fancy electronics of the Gen III, but I kinda prefer it that way.