Well, I guess I'll throw out a somewhat subjective review...
I've had both, I like somethings about each better than the other, and those things balance out. Overall I like the 08 a little better than my 04 mostly because it is a bit more comfortable for my long legs than the Gen1. Handling on both is great, I ride with mostly sport bikes, they're always surprised by the FJR. I like the longer gears a little better on the Gen2, seems better suited to the large amount of top end power the engine makes. The 04 was more snappy, easily power wheelied in 1st gear with exhaust system, but the 08 seems to make speed perhaps a little better because of its longer gears.
The 04 was slightly quicker steering and easier to flip back and forth. 08 might be a bit more stable at higher speed sweepers. They're very similar though.
Heat was minimal on the 04 here in MN, and never a problem. Gen2 has zero heat.
Airflow is improved on Gen2, a little less back pressure when shield is up, and a bit smoother everywhere else.
Brakes are stronger on the 08. The small application of the front brake when using the rear is actually pretty nice. Pads are more expensive but seem to last forever on these bikes, 26k miles on the 08 and half or more of the pads are left all around...
Fuel Injection was spot on with both bikes, though I do get 2-3mpg better on the highway with the 08. I like the mpg and temp display on the 08, but you give up the ability to view a tripometer and odometer at the same time, who cares though?
Stock seat is more comfortable on the 08 no doubt. Spencer mod on the 04 made it about as good as the 08. Stock 04 is too soft, spongy.
Best thing about the 08 is that it's pretty much the same bike as the 04. Oh, and no ticking either...
Some bike porn:
And compare FJR^ to a Concours. I don't even think the most die-hard concours owner can say their bike rates anywhere near an FJR in looks..
04 is probably better looking and best looking FJR ever made, but the black gives it a good run for its money! I like my tinted Cal Sci screen.