If I were in your shoes, getting an S1000RR would drive me crazy. I wouldn't want to be riding around on the freeway all the time on a bad ass high performance machine like that, and then when I finally get out to the track to let it rip, have to switch over to a lesser bike. IMO the track bike should always out-perform the street bike. What's the point in buying the extra performance when you don't get to use it?
I say get a sport tourer. It'll be a lot more comfortable, and you can ride it just as fast on the weekends in the mountains as you can a super sport.
I agree. SV650 for the street and R6 on the track for me.
That said - with your situation - I'd want the Ninja 300, or maybe an adventure tourer. My V-Strom is great for commutting. Has tons of torque, super comfortable, have a top case that holds a ton of shit, gets decent gas mileage. Suzuki build quality is meh, but it's so cheap compared to the BMW GS it makes it worth it.
I was going to suggest and adventure tour bike as well. I just didn't think the OP would go for it. If he has an S1000RR in his head, I don't see him settling for a V-Strom or Versys.
I commute on a VTR250 all the time and I don't understand why people find it so objectionable to "wring its poor little neck". I turn 8000-ish RPM at 70mph on the Honda, and while that's only about 5k from redline it certainly doesn't hurt anything.
I'm always reading the same thing from people badmouthing 250s, "You'll be wringing it out all the time". That's exactly why I ride a 250, so I can run it like a racebike every second I'm on it and still keep a safety margin via handicap. The fact that it get 60mpg and is fairly comfortable (albeit not in a lounge chair manner like the sport tourers you mentioned) doesn't hurt either.
You're right, it's not hurting it.
But to have that little motor buzzing between your legs is obnoxious to a lot of people.
Secondly, when you are turning 8k at 70mph, what happens when you open the throttle to the stop? Does it pull harder and harder as it moves through the powerband or does it slowly gain more speed? What about if you drop down a gear and go wide open? Does it take off like a rocket or does it bounce off the rev limiter? Now what happens when you are on the freeway in the 1 lane, someone is tailgating you and another car tries to change lanes into you? I'm not saying riding a 250 on the freeway everyday is certain death; but many people like knowing they can use the power to get them out of trouble.
I'm not badmouthing 250s at all. They are fantastic little bikes. They are cheap to buy, cheap to run and are extremely capable. It's the reasons mentioned above that people don't consider them ideal freeway commuting bikes.