I flew the X-Plane flight simulator from 1998 to 2002 and loved it. But soon I was longing for the real thing and in 2003 I bought a second-hand Kitfox III aircraft, after passing my license, of course.
My instructor told me that I was a quick learner, something we attributed to my experience with the flight simulator. But, to be true, I was flying on the simulator only light aircraft and with both stick and pedals. For example, the side slip by crossing the controls, was something natural to me. The X-Plane simulator is also more accurate when it comes to the aerodynamic model than Microsoft FS.
A simulator can't teach you to properly fly visual. Even high end professional simulators can't do that; our perception of the 3D world is something that we learn from the day we are born and is based on so many details we don't even think about. For example, you can perfectly keep your car on the road, even if you don't focus on it.
One thing the simulator is good at is the procedure training. Since 2003, I have modeled my Kitfox in X-Plane and have a true copy of my instrument panel. I occasionally train IMC conditions using the GPS and my turn coordinator to keep the course. Of course, I can't fly IFR with my aircraft but, at two previous occasions, I found myself in IMC without expecting it. It takes a while to get out of it and ... with a bit of training, you don't panic that fast.