Tone is three things:
1) Your comfort with the instrument, how it allows you to communicate, and the language you choose with your hands.
2) Wood. Neck woods, body woods, and how they're crafted together. Each *piece* of wood matters much more than the type, sort of. I've played with "lively" pieces of softer wood, and "dead" pieces of harder wood. The way the wood grew, including how the cells lined up during growth, matter quite a bit. I firmly believe that as the wood cures (and is broken down over the years), the cells in the wood will vibrate and break down to resonate more perfectly. The way we play the instrument over the years affects the tone; I have no doubt. If you've ever played an old guitar that was played lovingly by intent musicians, and then played the same model that was kept in a closet for 50 years, there is an unquantifiable "quality" that exists.
3) Electronics, strings, and hardware. All of these shape how we seek to amplify the acoustic qualities of the wood. If that means high gain rock where teh body could be plexiglass, then it does. How *much* the hardware affects the acoustic sound of the wood is a choice. What characteristics the electronics amplify is a choice.
All in all, an electric instrument is one of last true "mythical" connections in modern life. It contains elements of nature and elements of human invention. How those aspects are respected, and to what degrees they are emphasized and made to compliment each other are only important as they relate to our one-foot-in, one-foot-out of the world process of musical expression and creation.
-Mark