There’s pretty strong consensus that the FZ6 is a great second bike, but not a very beginner friendly ride–not just a view here, but on the FZ6-specific forums as well. While Yamaha has played up the beginner angle on the new FZ6R in its marketing, it’s not at all clear why the bike will be any friendlier to first-time riders.
It is clear where they cut some corners on the R to lower price. And the detuned-for-torque engine will put power further down in RPMs, where more casual riders are looking for it. The FZ6’s inline-four was known to give a sudden umph higher up in the RPMs that might get inexperienced riders in trouble, and the retuning of the engine could result in a more consistent and predictable throttle. But it’s just conjecture on the ride dynamics of the FZ6R–last I checked, they haven’t shown up at dealers and won’t for another month or two.
If you’re seriously looking at the GSX650 and FZ6R, I’d put the Ninja 650 in the mix. Yes, more power than the 500, but if you’re looking at new versions of the bikes, the new 650 has a lot of promised nice refinements, while the 500 has really been left behind in terms of development. Personally, I’d go with a used 250 for a few months and then go up to the Ninja 650. With the Ninja 500 it seems like you’re getting the worst of both worlds: a bike with power that can get a beginner in trouble and at the same time shy enough on power and updates that you’ll still likely want to upgrade the bike soon.