I agree on the tranny. Apparently the new 6 speed has a taller 1st and 2nd. I'd like a test ride before commenting much further but I'm not sure having a 6 speed for the sake of having a 6 speed is progress. The 5 speed is pretty good.I could do without the 6 speed...but the rest of the package is good!
I believe this still falls under the Gen III category (2 significant upgrades to engine, firmware, suspension, and/or fairing from the original 2003). But Yammie does adjust certain features of the bike over diff model years within each Generation. For example, the 3rd Gen debuted in 2013. In 2014 they updated the cruise control firmware (no longer an 85mph limit, IIRC). In 2015 they put out the uninspired Liquid Graphite color, with no other changes. Now in 2016, Yammie has incorporated some medium-level updates to the drivetrain and lighting--but I don't think they'll call it Gen IV (my opinion).
And yes this is still Gen3 from what I understand, not that Yamaha has ever referred to the various upgrades as "Generations" anyway. The Gen 1,2,3 thing seems to come from Yammie forums