gen2 is more refined. Just look at the dash, the fit and finish. It's just all around nicer. The tail section is questionable ... looks odd to me, but the rest is nice.
gen2 makes a bit more power, has a bigger engine, and is smoother than the 1st gen. The brakes are also better.
With that said, you can get a low mileage gen1 with mods and low miles, and save yourself $10,000 or more over a similarly equipped gen2... thus this really will never be an apples to apples comparison.
I didn't think the gen2 was worth the extra $$, especially given how fast they depreciate and the terrible shape the economy is in (resulting in great deals on used bikes).