More comfortable? Where'd ya get that? The Honda has a larger fairing and greater wind protection, to go with a quieter electric shield, adjustable seat ergos and V4 engine smoothness.
Areas where the Honda beats the Yamaha:
1-Build quality
2-Luggage capacity (35 litres per bag vs 30 on the Yamaha)
3-ABS option
4-On the fly adjustable headlight
5-A shock that won't have the headlight pointing at the sky when loaded two up, due to the Yam's too soft shock.
6-A truly adjustable preload for the shock, vs the Yam's two set settings.
7-Much better electric windshield
8-Three year unlimited mileage warranty, including Roadside Assistance for three years, vs the Yam's one year warranty which doesn't include Roadside Assistance.
9-Unique V4, vs yet another I4
10-Adjustable seat height
11-7.7 gallon gas tank vs Yam's 6.6
12-Adjustable instrument back lighting
13-Ambient air temp display
14-Easier valve adjustments (though more frequent)
15-Stereo option
16-Honda parts availability, vs Yamaha's
17-Availability this year, vs Yamaha's lack of availability for anyone who doesn't already have their deposit down.
18-Yamaha's next batch of FJR's (the ones beyond the presold first delivries) will NOT include the hard bags as standard.
That's just a few areas where the Honda reigns supreme over the Yamaha, off the top of my head...