I read a really good article about what makes the guitar tone really work on the Strat-O-Blogster guitar blog. That blog is by the way one of my daily reading blogs as it has tons of good postings about issues in the guitar world.
I think musicians over the ages have known about this, at least the ones that take this seriously. Orchestral musicians are trying to find the best instrument, intonate it and keep it in tune. Most of what they do comes from the brain and fingers, not from a huge pedal board in front of them — that would be a funny thing to see an orchestra performing, tangled with tons of cables and blinking lights.
It is also true of keyboardists and synth players — just keying another patch that sounds interesting does not mean that the whole performance or song should rely on a sound. Ultimately it is really the expression that counts. As the guitar is an extremely expressive instrument, this is why you hear the difference between a guitar artist and non-artist by just giving them the same guitar and amp and hear the difference.
Anyway, only way to get to this point, as the article mentions, is to just focus on a good instrument and then develop your style — woodworking but worth it.