It probably has something to do with the sheer number of controls needed. I don't know whether those later games in the series "streamlined" things any, but in TIE Fighter Collector's CD-ROM, the various commands took up the majority of the keyboard. It can't be easy using a controller -- typically requiring two hands -- and still freeing up a hand once in a while to use whatever commands aren't mapped to the buttons/sticks/triggers (there would almost have to be at least a few that wouldn't fit). By contrast, a decent joystick should be useable with one hand, at least much of the time, leaving the other hand free to use the keyboard.