The KLR has the advantage for girth, whereas you can load it up without interfering with your riding position. Both bikes are much improved with aftermarket suspension parts but the DR is far superior to the KLR off road both in suspension and frame geometry. The stock DR also has the advantage for trail riding considering its power band, not so much more power but easier to use off road. My experience is that the DR has a great low end with a substantial boost felt in midrange whereas the KLR is simply a mild increase throughout the rpm range. But then the extra weight may be responsible for that feeling. I own both bikes and neither are stock suspension or power wise anymore. My DR is a better bike than my previously owned stock KTM 640 both handling and suspension are better but the DR has RMZ forks and Cogent rear shocks and much work done inside the forks. Power wise the DR is at least as good as the KTM was. I bought the KLR for my road trips since I wanted a bike that was capable off road. It serves that purpose perfectly with a 688 piston and suspension components. In short my DR is a 650 enduro and my KLR is a 650 (688cc) dual-sport completely suitable for road trips. I used my DR for many 800-1000 mile road trips before buying the KLR. The DR is smoother than most 650's and though they say the KLR is smoother when using the 688 piston it is not as smooth as my DR was stock or is now. Vibrations of neither bike bother me in any way though.
Chrome and noise are no reason to ride a motorcycle!
:2002 KTM 640 DS :2003 Suzuki GSXR1000
:2005.5 KTM 950 :2007 VStrom 1000
:2008 DR650 :2009 Aprilia DorsoDuro
:2009 KLR 650 :more to come