the pros of a bolt on neck is that if it gets warped or broken, you can usually get a replacement for it. cons, the only other than sustain is a more percussive sound and maybe a larger neck joint making it harder to get to the higher frets. although some manufacturers are making the heel easier to use. for set neck and neck through, cons are if they get warped or broken, the whole guitar must be replaced. these add some benefits too. set necks offer an increase in sustain, with a choice of materials (you can have a mahogany body with a maple neck, or alder body and mahogany neck). sometimes the heel is bigger than the bolton since you have to have good support. some are smaller. neck thru offers great shaping for good access to the higher frets since there isn't a heel. with the material going all the way to the end of the body, the pickups usually get their tone from the wood around them. so you have to choose the wood wisely, that can be a pro and con together. with a neck thru design, you can scale down the thickness of the body better and do some really cool stuff to get a good feeling body. i would think that if the neck is thinner (less material from headstock to bolt area) there might be more sustain. as for getting more sustain out of a bolt on guitar, lighter gauge strings may give you more, as there is less mass to move. check your pickup height too. if they are really close to the strings (especially single coil) that could have an effect on sustain as well. if your strings are really old, if i remember right, that can effect sustain as well. if you action is really low, where it is buzzing against the frets, that will also. there is nothing wrong with low action, as long as it is done right. going back to string gauge, thicker strings may give you more sustain since more mass will take longer to stop vibrating i think. that's about all i can think of.