I've asked around, and it seems all flight training programs use a combination of flight simulators and aircraft flights to train pilots. This works well for most pilots who fly airliners which don't spend much time in turbulent air or close to obstacles, and the flight simulator aerodynamics are very close to what is experienced in actual flight.
My question is where do the flight simulator aerodynamics models breakdown? I was wondering this in relation to rough air flying skills, where the aircraft or helicopter flow field interacts with surrounding environment (like inside a convective storm or near obstacles like trees and buildings) I would imagine these are situations that are hard to model since it depends on accurately modelling the interactions, which are difficult to run quickly enough for running a flight simulator. Fixing this by only doing flight training seems dangerous, especially for newbie pilots since the margin for error is very slim.
Personally, even though its more expensive than a flight simulator, a first person view drone would be a good intermediate step between the flight simulator and full scale training, with the response characteristics and control interface being the same as the full scale aircraft or helicopter.
That said, I don't know where the flight simulator aerodynamics begin to diverge from what is actually is experienced in real life, so the drone might be completely unnecessary. I'd love to see how this problem is resolved now.