Having read the article (and leaving all the magazine bashing aside), what struck me is that none of the four bikes they compared ended up being ones that the guys really really liked. Even the "winner" -- the Connie -- didn't get unequivocal love. Granted I'm prejudiced, but as I read about what was problematic on each one, it struck me that my Gen II FJR kinda addressed all of them. Granted I've added a PCV and some other farkles, but except for throttle twitchiness until I added the throttle tube and power commander (it's an '07), virtually all of their issues -- ergos, fun in twisties, low speed handling, comfort, wind protection -- have been addressed by the FJR.
Did they not include the FJR because the result would have been a design not truly updated in 5 years would win out, if you did about $500 worth of farkling? I doubt that's what was in their minds but face it, it wouldn't do well on the "pushing people to buy new bikes" front if that were the answer.