I've got 120,000 miles on my '09 FJR. I'm 5'3, so it's about the biggest bike I'd ever want to ride. All gens have their issues, but most are relatively minor, or taken care of by recall. The early gen2s ('06-'08) had kind of a snatchy throttle and stiff throttle return spring. Those issues are better from '09 on. The seats suck on all years. Gen3s are working through engine light issues, triggered by a number of silly things: not turning the ignition switch quite far enough, shutting down with the kickstand switch and at least one more that I can't remember, but the most annoying part of this issue is the dealer has to clear the code and many don't have the correct adapter to do that. A small percentage of gen1 bikes had valve guide issues. Cam chain tensioners have plagued both gen1 and 2, but it seems the current CCT is a winner with no reported failures. '6-'09 bikes had a ground wire terminal block issue, fixed via recall, but many of us feel the recall wasn't comprehensive enough.
Overall though, any year FJR is going to be a runner and you'll probably never wear the engine out. I know a guy that put just short of 400k miles on a gen1, with no major engine work.