Gooseneck is a better choice when you get off level a lot. I've had my stock trailer leaning at crazy looking angles. You have better articulation with the ball, and the frame is up away from the bed rails to the point that rail clearance isn't even something you think about with most goosenecks.
Even with a permanent gooseneck installed in the truck, most of the bed is still usable so for people who typically use their truck bed a lot, a gooseneck is more convenient.