Pros and cons, should also include set neck as well.
I have all three types in various body styles. Most of my neck through guitars are similar in shape to a Stratocaster. I have three set neck guitars, one similar to PRS, one similar to LP and the other is like a double cut LP. I used to have a negative bias towards bolt on necks that I had used for 17 years. I sold most of them and the last one I kept did not last the test of time. It all depends on the quality of materials and workmanship of the instrument. That being said, Pros for bolt on, you can replace the neck vrs a neck though which would be impossible to replace and expect the same guitar to be returned, sure if you are willing, the body can be cut and glued onto another neck assembly (fools errand). I would say another issue with neck replacement with bolt on type, matching the neck angle and scale (which is probably a standard based on Stratocaster design. Considering the issues I had with bolt on necks, they always came loose. Just about every bolt neck guitar had shims under the heel of the neck. To me that is not a good transfer of energy. Then again, they were inexpensive to start with. I now have a new bolt on neck and I am impressed with the overall quality, tone, and playability. I am also positive there are no shims between the neck and body on this one. Sustain is similar to my other neck though and set neck guitars. Resonance is more of a factor of the tone woods used in the body of the instrument as well as energy transfer of the neck and neck joint. However, bolt on neck guitars may also suffer spits in the wood of the body around the neck pocket. Again, that is related to type of wood and how well it is cured before assembly. The same would apply to neck though and set neck guitars. You do not always get what you pay for (though distribution or places like guitar center with high margins). I would agree with the pickups as well as the bridge assembly. Unplugged, my bolt on neck guitar has about the same resonant energy as my set neck LP type guitar. My neck through guitars do not seem to exhibit the same vibrational characteristics.
Then there is the neck straightness. I normally keep my necks flat with a very minor upward bow if at all. Setting up a bolt on neck may be more difficult if the neck is not a tight fit in the pocket (even worse when there are shims).
I doubt that I would go through the trouble of removing the strings and disassembly of the neck on my bolt neck guitar. Getting the strings back on and tuned is more trouble since I have a Floyd Rose on it. Reason why I mentioned that the bridge also contributes to the sustain factor. I have played many other guitars with Floyd Rose bridges and I was not impressed. But the one I have now is incredible. I believe the key is in the body woods (thick maple cap over alder body). It all becomes subjective anyway.
Set necks, if there is a weakness in the tenon or loos fit, may also be in relation to tenon length into the body of the guitar that makes a difference. Pro would be good transfer of energy between neck and body (all depends on design integrity). Con would be cracks in finish around the heel of the neck. Con, neck heel can limit fret access which depends on design once again. My LP type guitar has no heel, since it was carved and blended into the body which provides a smooth transition. Bolt type guitars will always have interference where the neck meets the body. Some guitars will have some relief as well as contoured cuts to improve playability of the guitar.
Neck Through: Pro, no heel on the neck, completely contoured. All depends on the body style. Con, choice of neck wood will dictate overall tone of the guitar. There are some MFG that have top wood choices (caps that cover the body of the guitar and in some cases cover the neck wood) that will influence the tone of the guitar to some degree. Benefit for bolt on neck guitars is that the body and the neck can be made of different woods. Same applies to some of the set neck guitars where the neck wood may be maple and the body mahogany or any combination of various woods if available. This usually only applies to Custom builds (of course will have a premium for that service). I can think of one company that only builds custom guitars based on your choice of neck woods, fret board, body woods, etc. would be Carvin. There are other brands like SUHR guitars, Roman, Tom Anderson (just to name a few).
I generally prefer neck though guitars, but I also like my bolt on guitars an set neck Guitars. They all have their own unique tone, character, and playability. Actually I recently ordered a new bolt on guitar and I am eagerly waiting its arrival.