Played GranTurismo or Daytona for years, but didn't develop a habit of driving over curbs at 150 mph when I'm in my car
Seriously... FS is a good videogame, but take it for what it is, a videogame ! Up in the air it's so different, the noise, the vibrations, everything really, that you can't even compare the 2 situations.
I guess FS can give you good instrument scanning skills, just make sure you don't abuse of them. It took me 1 lesson to fix that, since if I kept looking at them I would eventually feel sick ! Also, as soon as you realise that the traffic in the air is real, and it can hurt you, your instinct will make sure you are looking out of the window quite a lot !
If problem with FS is lack of rudder, you can get one of those joysticks with the twisting grip that acts as rudder. It won't get your feet working, but will get your brain to think about it. Once in the cockpit, you'll feel the pedals and it'll be quite natural to use them.
Good luck