BMW = correctly positioned engine and trans driving the correct wheels, AKA longitudinal and RWD.
MS3 = transversely mounted engine and FWD. By default, we lose all sorts of feel and control of the clutch and the shifter this way. However, I can offer a level of consolation for you. It gets better as you own it.
My suggestion to you is to get the short shifter immediately, and a rear engine mount. This will get the shifting back to a smoother level, and is my next planned mod. The engine mount will restore the buck/jerk feel that you are getting now. Also, you'll get used to how it drives, and learn to drive it more smoothly. Finally, swap the intake for an SRI or CAI, and that will improve the lag and also increase the smoothness as well. The stock airbox restricts airflow so much that the car literally is choking on its own lack of air. This means that its a very on/off feeling. That is until you do something about it and give it more breathing room. I just hacked the box, and it worked wonders for this.