Ah, the age-old topic of tone woods.
While I pretty much moved on from his guitars some years back, I think that Paul Smith has a pretty good understanding of makes an electric guitar tick. He had some pretty solid mentoring from Ted McCarty and has spent a lot of time and money on R&D. One of his favorite maxims is "everything affects everything". Wood matters. Finish matters. Pickups matter. Shape matters.
The key to making a great guitar is to treat it as a system rather than a collection of components. Some of our benchmark designs are happy coincidences...most of them, more likely. When people try to build a dream parts-caster with all sorts of exotic materials, the results often disappoint.
What's lost is the interplay between the pieces. I remember the days when sustain was the holy grail and mass was thought to be the key. People relished their 12 lb Les Pauls and added more mass with brass nuts and brass bridges. The science behind that approach was replaced with a new truth that resonance, not sustain, is the end all be all. Next time you turn around, conventional wisdom says pickups are all that matter since they're amplified instruments.
What's the truth? To me the truth is that there's no objective standard of beauty. Beauty can be a happy accident or it can be manicured at the molecular level. In either case, there's no sure recipe. Where companies like PRS are excelling is in making things consistent: of the six PRS I've owned, I bought five of them sight unseen. Of those, only one wasn't a great guitar and, ironically, it was a "handmade" '89 model. I say they're great guitars but I've sold off half of them and somewhat ignored the others because they don't appeal to me as much as the others.
One of the wonderful things about guitars is that they're more tactile than most other instruments. Plucking strings, fingering strings, it's arguably more intimate to play a guitar than about any other instrument. Something so very personal is going to be inherently subjective. Tone woods matter. Pickups matter. At the end of the day, everything matters and if you're lucky, the whole is greater than the sum of the parts.