The whole purpose of a robotics environment like this is so that robotics builders can concentrate on actual robot stuff, whereas MSRDS makes you waste so much time learning their proprietary formats & techniques that you could easily loose the fun in learning robots!
(disclaimer: not a robotics guy, I just messed around with an NXT set last year)
My main issue with their environment is that the resulting robot doesn't actually do any of the thinking, you need a PC running MSRDS connected at all times. All processing is done on the PC, and commands are sent down to a slave program running on the robot. Other development environments supporting the NXT (like NQC) target the brick directly and give you a fully-independent robot, which is (to me) much more interesting.
Their realtime 3D simulation environment looked like a big selling point, but then I couldn't make it do anything myself besides running built-in samples. As you said, MSRDS focuses on the wrong thing, because NQC (or even the built-in Lego software!) was a lot more fun.