Well, it is a matter of habit. The first time, sure, playing with joystick is painful while it is about precision. But the more time you play with, you'll get acustom with and be better. There are thing you couldn't do with a mouse like doing some sort of super maneuver and well you don't have force feedback with a mouse.
I should probably clarify that when Freespace/Freespace 2 first appeared, I played them with a joystick. Trust me, I know what a good joystick feels like, and have probably logged a thousand hours of my life into various flight & space sims with a joystick.
I'm not sure what "super maneuvers" you're talking about, but with a mouse and a smart keyboard mapping I feel like I can pull off all of the moves I want, without sacrificing precision, even in a 6DOF environment (Which neither WCS nor Freespace is). This gets even better if I can use the toggleable scripted mouse, and switch between "Freespace-Style" and "WCS-style" mouse flight at the click of a button.
That said, I can't argue with the fact that joystick (especially HOTAS) just plain feels cool and can be lots of fun.
I've just discovered that it isn't for me, and that mouse+kb is perfectly viable and effective.