I've also been flying flight simulator for years (even before getting my PPL) using my right hand on the stick. I can't fly it with my left hand no matter what.
However, I fly my RV with my left hand on the stick, and it feels natural as can be.
I use my right hand for throttle, radios, writing ATC instructions, changing songs on the ipod, getting a drink out of the bag, etc... all while keeping the left on the stick. I wouldn't want it any other way.
I flew an FA-18 sim (one of the real ones

) a couple months back with left throttle and right on the stick. This also felt just fine and was an easy switch, but I wasn't fiddling with radios or anything either.
--Clay