First of all, let me say that I'm really grateful to the Flightgear community, I learnt a lot through FG about how to fly a plane.
I found most of the defaults hard to use, including simple things such as the steps in which the throttle or rudder increment when you use the keyboard. And with the joystick, I found the default configuration sorely lacking. I had to setup rudder trim, elevator trim, flaps, propeller mixtures...pretty much everything other than the basic flight controls on the joystick.
It took me quite a few months before I could get everything setup to fly well. I feel this is a little too much time for a typical user. I'm one of those crazy guys who won't give up until something works, but I don't expect many people to have this level of patience.
