Echo Genghis. Hand-flying is a motor skill, learned and hard-wired into the brain, in effect. That's why I suspect my FI instructor told me that it's important to get the first 20 hours right - get those right and everything else follows. There is a danger with desktop sims (as indeed there is with any sim) that your first 20 will be corrupted in some way with negative learning.
As an indication of the potential adverse influence with a 'simulator', the device I used for my IR tended to roll before it yawed when an engine was failed. I therefore watched the AI rather than the DI to catch the inevitable fail on the go-around from minimums, using aileron then rudder. This most definitely WOULD NOT WORK in the real aircraft, where yaw came first and required the correct strategy (rudder then aileron).
I have heard it said that MS FlightSim is of benefit for more advanced training, in particular the IR. I didn't find that to be the case and stuck with RANT.
Get flying, especially for the first 20 hours.
Personal view only, ready to be shot down by proper pilots
