The R3's rear shock is softer than the cbr's, so the ride is a bit more bouncy. Everything is a bit smoother on the R3 (clutch, gears, vibration etc). Clutch is heavier on the R3. Other than that they ride pretty much the same to me.
First, I'm still a new rider. Also, I don't like the aggressive riding position on all the 600's I've sat on. It hurts my back and neck. With the R3, I get to have a sport bike style and a relaxed riding position. Win! Sure I don't get the power of a 600, but I did get a 60% power increase over the cbr 250, so I'm still happy.