I wonder why people continue to compare bikes that are in (mostly) different categories. The Futura resides at the sporting end of the sport-touring continuum (sp) while the FJR is clearly at the touring end of same. While the Yam. has significantly more HP, the Aprilia is ~80 lbs. lighter (540 vs. 620, wet). Not an insignificant amount as long time riders know. Also, the riding positions of these two are totally different. The Yam. is bolt upright while the Futura is much more sporting.
The trade-off is this. The Yam. may be a better very-long distance mount by virtue of wind and weather protection but for me, the Aprilia will be more fun to ride 90% of the time due to its superior handling, excellent low and mid-range torque and even its peak HP of 100 is more than adequate (yields 1/4 mile times in the mid 11's if I'm not mistaken). And it has standard hard bags as well.
I see I have digressed. AFAIC, the FJR should only be compared to the Honda ST1100/1300, BMW R1150RT and the Concours, though I may have overlooked one or two.