The forward controls of the second gen, along with the pillowtop seats make it more comfortable on longer rides. As far as the fairing goes, I've not been able to notice any real difference. For me, 8 or 10 hrs is the most I've done in a day and, regardless of whether I'm riding the first or second gen, it's always my shoulders that begin to ache. Butt feels better at the end of the day when I'm riding the second gen. I've not noticed any real difference two up either, other than, ...with the stock leveling links....the second gen gets a bit squirrely in parking lots two up.
I think a good way to describe it is that the first gen is a sport / touring bike, and the second gen is purely a touring bike. (That looks derned good in the process)