I'll probably catch hell as a noob, but here goes.
All mechanical things have issues. Some are recalled or campaigned, some are not. Sometimes the design is improved and if you want those improvements you need to make a purchase. BY and large I don't think there is a better bike out there than the FJR. I'll let ya know if I change my mind when my new Super Tenere finally arrives.
I don't have the miles some of you have, 43k on my '05, and I am certain I will regret writing this, but not a lick of trouble. I piped it and have a PCIII which may have corrected any throttle response issues, beyond that NADA, zip, not one single hiccup. I will likely research the CCT thing and replace that at next valve service.
As I learned over on DucatiMonsterForum, any survey or poll must have ****ies as an option. So I did not vote.
Oh yea, some of you guys have some serious issues. I like it here.