The main difference is that the pickups are mounted in the neck (well, the extension of it that goes through the body). This tends to make them brighter sounding guitars. However, every guitar is different and I have always been of the mind that you treat guitars, especially non-factory machine cut guitars as individuals. I've got bolt-neck, set-neck, and thru-neck guitars and they all have things about them I love and they are all different sounding. I don't know what percentage of that is the neck joint, I suspect some of it is but not an extreme difference because of the neck joint. Bolt neck guitars are easier to work on - that is one definite.