I second Jame's recommendation. It's hard to find a lighter dual sport bike with enough fuel capacity and comfort to handle daily commuting, and anything much bigger than a KLR will do less well when off pavement.
And as an example, I just spent time a NW Mogfest with two longtime friends who rode down from Calgary (1500 km), him on a Ducati ST3 and she on her KLR. They carried all their camping gear with them.
The KLR has been made forever and it will seem old fashioned, but won't cost the same as something more exotic like a KTM. Even better, though, is the enormous amount of support for the KLR . . . all problems have been identified and documented and the aftermarket has provided hundreds of useful modifications. If you want to farkle your own bike as a hobby, buy the basic bike and have at it. There are, however, a whole bunch of KLRs that have lots of very nice modifications that have already been paid for and installed. Check KLR.net or the classified section at ADVRider for some of the best:
http://advrider.com/forums/forumdisplay.php?f=52.
Nothing wrong with a 650gs. It won't be as good in the dirt, but would probably be better for commuting. It won't, however, be as cheap for any given model year, and it won't have the level of support that exists for the KLR. (I suppose you make anything for 25 years and they'll be support and a following.)