I switched last December. I had put 16.5k miles on a 1st gen Ninja 650R, and I've put just over 12k on my 2nd gen Versys.
The Ninja is quicker, the rider gets less buffeting.
The Versys is more comfortable, less blown around by the wind, and has less vibration.
Also while the stock suspension on both is lacking, the Versys gives you more to work with for upgrading, at least in front. I think the rear shock on both really needs replacement.
The Versys has much longer range. On a good tank of gas I could get 185 miles or so from the Ninja with the fuel light on for awhile. On the Versys I've gone to maybe 224 miles before the fuel warning was steadily on. And a lot of people seem to get better fuel economy than I do.
I had dealt with the vibes on the Ninja to make it comfortable touring, but at 7k RPMs the vibes would still remind me not to cruise there. I get no such "warning" from the Versys. Much smoother. Maybe the new Ninjas with some rubber engine mounting are too?
The US 2012 Ninja 650R while awesome in many ways, isn't easy to install luggage on. That would be a deal breaker for me. Fixed in the 2013 model.
I loved the Ninja, but I enjoy riding the Versys more, and it's a better fit for me right now. Still I'd know I'd love to have a 2013 Ninja 650R.