I might not be the best guy to listen to. Once I rode a KTM I haven't looked at much else.
Having owned a BMW GS and several other Japanese bikes, Id say I have a good basis for my opinion. I have also considered buying a 640 or 690 to share ride time with my 990. I really like the idea of a light weight all rounder for rides like the TAT, and some local area dirt stuff. I love my 990 but sometimes a smaller bike would be nice, and at this point the 640 or 690 would be my first go to bike.
They both look to be well set up and clean. They are hard to find in my area so 2 to choose from is nice. Id say the lower mile bike would be my first choice for obvious reasons. Although the higher mile 640 has been well set up and those add on's are pricey. So setting up the more virgin bike could get expensive if that the direction you go. Id say my first choice wold be the KTM with the KLR a far second and the BMW even further for me.
The KLR is a great bike but maybe not as high quality as the KTM in regards to riding in the dirt. Can it go any place YES will it be as fun as a KTM NO. My brother and I had one for a while. Is was a good bike simple easy to ride. Reliable. Just a good all around dual sport.
As for the BMW they are sorta great bikes. They do most things well.
The price difference from a KLR to the BMW or KTM is substantial but Id still spring for a KTM personally. I just like them, They make you smile.
This is all just my opinion. Once I rode a KTM I pretty much was sold. So I hope nobody cracks me to hard.
2006 Toyota Tacoma Ute.
1994 LandRover D1
2008 KTM 990 ADV-sold
1972 Toyota LC FJ-40-sold
1992 SWB RR Classic-sold
2006 BMW GS1200-sold