The clickable cockpits seemed to me to add a little more to the experience. Instead of pressing CTRL+whatever to do something, you actually found the switch and activated it. It's an unecessary feature, sure, but I always liked it. For modern sims, though, I agree that the time lapse for using the mouse is a problem, but I think that Falcon 4.0 did a good job by adding that freeze mode, so you could find the right switch and use it without using precious time.