First, you're comparing a beast (multi-cylinder bike on this forum) to a bit more dual sport thumper (single cylinder) bike. Further, you posted in the Beasts forum, not the Thumpers forum, so I guess you're fishing for what you want to hear. The closest competitor to a F650GS is really a KTM 640 Adventure, but even that isn't too fair. The Rotax engine in that F650GS is a nice, smooth piece, especially compared to the LC4 engine in the KTM.
I've been going through the same thought process, but for an adventure bike to add to my 2 stroke dirt bike. For street only, and a little exploring, get the Versys. If you really want to ride a mix of road and some offroad (gravel roads, 2 track, occasional single track), get the F650GS. If you want to do even more offroad, land some decent jumps, etc., get the Dakar race replica KTM 640 Adventure and live with some vibes and euro backwardness of the LC4 engine.
Another indicator is tire selection and aftermarket support. The KTM runs standard size offroad tires with tubes, while the other bikes run street size tubeless tires. They all have good luggage and rack options now so in this group that's not a deal breaker.
1999 KTM 300 E/XC -- even better now that it's an Eric Gorr ported 310.
Looking for an adventure bike to add to it
Austin MotoSports Association www.amsaclub.org