It reads like your question is one of value - which bike is the better value? In that case, $9,500.00 is too much for that 2012, even new. There are plenty leftover 2015's out there for $10,000.00 and even a little bit less. $5,000.00 for the 2006 is the better value, especially if it has some accessories on it that you desire (after market windscreen, custom saddle, top box, frame sliders, etc). You could EASILY burn another $1,500.00 on these accessories.
IMO, the improvements to the third generation FJR (2013-2015) are substantial, and most here would agree with me. Whether those improvements would be valuable to you is hard to guess. If you have had FJRs before, you would definitely appreciate most of the improvements. Also, if you are planning to tour cross country with your bike, certainly the cruise control alone would be appealing to you.
I rode a Gen 1 FJR for 60,000 miles all over this country. I loved that bike. If money was an issue, and I had to change back to a Gen 1 (verses not riding at all), I'd do it in a heartbeat without even batting an eye. But my current Gen 3 is the best motorcycle I have even ridden. It's that good.
In the end, it all boils down to "How much fun do you want to spend?". Be that as it may, given two choices in your OP, IMO, clearly the '06 is the better buy.
P.S. - it doesn't matter where your thread is posted. The people here that really want to help you will find it, this much I guarantee.