a little guitar design 101:
Why is the neck joint so key? First, we know that pickups are not microphones, but magnets, converting a change in magnetic field caused by moving metal strings into electrical output processed to sound. Thus, the better the vibration, the easier it will be for pickups to do that conversion and send a hot signal to the electrical->audio converter, aka your amp.
How is this made easy? well, the string in question is fixed at two ends. these ends have a damping factor (if you hit the string it won't vibrate forever, due to air resistance and damping of the anchoring points). well, if you want the best vibration (sustain), the vibrational waves that travel along the string should be in sync with those that travel from endpoint to endpoint through the anchoring material (body, neck).
Now, we want this so that the waveforms do not cancel each other out as they travel through the instrument. If they take a long time to get passed a point, they will arrive out of phase and damping occurs. since the two anchoring points (nut, bridge) are often on different pieces (neck, body) the joint that connects these two things should be as seemless as possible.
imagine trying to pass a vibration through 2 pieces of wood bolted together, then through two pieces of wood smoothly connected with a secondary material (glue), or better yet, one piece of wood with no joint at all. these correspond to Bolt on, set neck, and neckthru construction.
and the body/neck material...the vibrations that travel also need to compress and expand the material at very small scales, so you want this material to be thick enough so that the atoms bump into each other when excited by the vibration but not so thick that it can't move when bumped. hence, i'm not a fan of plastic body guitars either. sure, again, use your amp, you can make it sound good. but why not start out sounding good? wood is generally a good material because it is dense, but not as completely dense as plastic. wood has pores. different types of wood are on different ends of this transmission spectrum and contribute to TONE. mahogany for example is denser, so it sounds deeper & warmer, while basswood is less dense so it has a higher concentration in mid to upper range frequencies of vibration. sure you'd think you want something really dense to get that thunderous tone, but then you factor in standing on stage for 2 hours with a heavy guitar. hence the tradeoff.
there's more but i won't get into it unless you guys want...
edit: I might add, though, the reason why all guitars aren't neckthru, is because if you break the neck of a neckthru guitar, it's fucked. you can't replace it since it's all one piece. hence the other options, if anything happens, all is not lost. they are also cheaper to make, at the cost of some sustain/tonality.