I own both a DL650 and a Ninja 650R, so I feel qualified to answer.
Hands down, the Ninja is a lot more fun. Very different acceleration of the parallel twin compared to the v-twin in the DL650. The Ninja takes off and accelerates. The DL650 just accelerates. The DL650 is not a sportsbike and I don't expect it to be one. Am I every disappointed with it's acceleration? Hell no. It puts a smile on my face when I want it to, and has gotten me out of trouble when I needed it to.
Lots more room on the DL650. Legroom and seating are better, in my opinion. The seat on the Ninja is quite firm, so not as good for longer rides. It'll be all right if you're just going to be carving corners all day. I'm 5'10, ~220 lbs and I look like a friggin' circus bear on a kids tricycle on the Ninja. While the Ninja does have an up-right seating position, it's not as upright as the DL650. Also, because of my upper body height (5'10 with a 30' inseam), when leaning forward I can easily look at the front of my screen. Wind hits me squarely in the helmet, which causes a hell of a lot of wind noise and some buffeting. 70+ mph is only bearable for short periods.
The DL650 is the much better bike for two-up travel. The suspension is setup much better for it than the Ninja, there is more seat and legroom for the passenger, etc. I take my wife out a lot on the DL650, and wouldn't even think of using the Ninja. It's just not made for it. Me at ~220 lbs, the wife at ~150 lbs, loaded up, and it still performs very well.
The 650R is nice and flickable, as it's smaller, but I've found the DL650 a heck of a lot easier to control. While slower, I feel more in control on the DL650. It's much smoother and compliant. The Ninja is definitely more responsive I guess.
Wife's (though I ride it more often right now):
If I had to chose between either of them, it'd be the DL650 every single time.