Bolt-ons have a certain snap in their tone. Setnecks have smoother tone and they're easier to play from the higher frets. I have one of each and I think that only music where a bolt-on is better is metal. In metal the setneck seems to lack some attack (that certain snap) but it's not bad in that either. This is the basic difference between them but you should also take the materials into consideration. It's not all about the neck joint type. There are some wood combinations that at large go with a certain type of guitar.
Plus the scales... You don't see a 24,75" Bolt-ons very often and vice versa you don't see many 25,50" setnecks.