I have a F650GS (twin), which is similar to the F800, and a R1200GS. I've ridden my friends F800GS a few times.
The F GS's feel much lighter and are great bikes. My F650GS feels about like a KLR 650, only with power but not as much weather protection. The R1200GS has much better wind protection with it's nicer windshield, tank shrouds, and cylinders. Nice not having to deal with a chain also. I like the Telelever front suspension on the R1200 better than the traditional forks on a F800 but others may not? The stock seat on the R1200 is pretty good the one on the F800/650 is horrible. There are options just be prepared. Center stand and hand guards may be options on the FGS too.
I found the F800 with it's 21" front wheel to be a bit more "twitchy" or less stable than the F650 (or 700), certainly less than a R1200GS at speed. On rutted dirt roads and worse either F bike is nicer than the heavier R1200GS.
Not sure of your price structure but in the US with a $4- $5,000 difference in price the F800GS may be the better value. Factor in a seat, center stand, hand protectors though. Overall, certainly on roads, the R1200GS is the better bike IMO. The new water cooled GS should be even better.