No doubt Ken.. The sim can lead to terrible habits. I have seen guys use all sorts of techniques to handle the sticks and some who are satisfied with some really ugly ways of getting a plane from point A to point B. Most are not a huge deal unless you get into competitive precision flying. Bad habits are exponentially magnified at that point.

I still fly with thumbs but I'm working to learn to fly with thumb and forefinger. Its clear to see that the guys who use the pinch technique or place their thumb on top of the stick and wrap their index finger around it have much better touch than I do. Im determined to make the switch and I will eventually.

To me there are two really bad and potentially fatal bad habits that folks use regarding takeoff.
1. Using ailerons to correct instead of rudder to setup for final approach. However, rudder is something you have to learn to finesse. Too much and you can snap right into the ground if you add in too much #2.
2. Using elevator to control rate of descent on landing approach. THROTTLE is the correct tool to use to set approach speed and angle/rate of descent.

If you want to land in 1 piece, learn to make 1 click corrections on the throttle to setup your approach. Only use the elevator in TINY moves and none if possible until the plane is over the runway and less than 4' off the ground ready to flare. This all comes down to your setup for your turn to final approach. You need to learn to judge the wind so that you are at the right altitude and right distance out.