I've ridden an '05 F650gs thumper, '05 R12GS, and now an '07 R12R. It really depends on what you're after.
For me, the R12R is superior when it comes to long range and long distance riding. Fuel economy is not as good as the 650gs, but if you have a light throttle hand, the R12R still does pretty darn good. I amazingly managed 339 miles to 4.8 gallons once. The boxer engine is super smooth, and having that little extra bit of power does help to get you out of trouble sometimes. The agility of the 12R is not quite as good as the 650gs, but the 12R can still carve corners if you know how to get off of the seat. Also, the electronics on the 12R (e.g. optional computer) really helps you with all kinds of information. The 650gs thumper doesn't have this. It's still pretty much a basic bike.
The 650gs is amazing in terms of fuel range. Without any mods, you can expect 60+ MPG even when you gun the bike most of the time. It's pretty hard to get the bike down into the 50 MPG unless you're insistent on riding in 3rd gear every where you go.
When I had the 650gs, I installed a 43 teeth rear sprocket (45 teeth is standard) to smooth out the bike while riding HWY speeds. It really helped to reduce the engine vibration and made the bike much more comfortable at higher speeds. Of course you lose a bit of acceleration (bottom end) from decreased rear sprocket size. Then again, you're still much faster than the majority of the cars out there, so it's OK. Taking the rear sprocket down by 2 teeth drop the RPMs by at least 500 RPMs (if not a little more). The side effect to riding at 75 MPH with less RPMs is pretty cool. The bike's fuel range increased to 74+ MPG city and nearly 83-84 MPG HWY. On one trip, my older brother with his rear sprocket modified f650gs did something like 97 MPG. Insane!
Regardless of rear sprocket mod, the 650gs can never be as smooth as the 12R. As a result, the 12R will allow you to ride much farther and have less fatigue in terms of vibration. Of course this also means you have to get a decent windshield so you don't get blasted off of the 12R when you're doing 80-90MPH. When it comes to turns, the f650gs will dust the R12R any day. Enduro bikes are built for agility. My bro kept on hugging my arshe as I was taking a turn. Of course he had to play catch up when I'm out of the turn.
As for the concern for the additional power of the R12R, don't worry too much about it. The paralever and telelever combination has the bike so stable that a minor lean forward will prevent you from flying off the bike. This is also the reason why BMW has the default sitting position slightly leaning forward. Yup, they do think of everything. I actually felt more acceleration on a 650gs than on the 12r. This is mostly due to shock compression rather than a power factor. If you tell me I should have increased the pre-load, I would say, "yeah... maybe I should have done that."
My recommendation would be, go for the gold and get the 12R. You won't regret it. However, if you do plan on getting on the trail one of these days, stick with the 650gs. As always, ride your level and slowly grow into the 12R's power. After a while I don't think you can go back to a smaller bike. Good luck and cheers.
It's Chunky Smooth...
I have also looked at the Breva 750.
