PROFILECLIMB,
The most important part of IFR flying is having a good scan. The problem with using something like Microsoft FlightSim is that it teaches you to use a bad scan. Like another CFI wrote above, if you use something like Microsoft FlightSim to practice IFR procedures, you run the risk of having to unlearn a bad scan and learn a good scan. This can be a huge problem for an IFR student.