If you are considering having a luthier build a guitar for you then it would be a good idea to do some research on which tonewood you should use in order to accomplish the sound that you are hoping for. After the wood selection, the the rest is up to the Luthier and how well he builds and shapes the tone of the guitar..
As a side note let me say that if you are looking at a major manufacturers product (Martin, Taylor, Gibson, Taylor and many more) make certain that the specific model that you are looking at is a solid wood guitar and not a "laminate" guitar. Laminate guitars are layered much like plywood and therefore wood choice is simply an aesthetic choice.
Selecting the Right Guitar Wood
The sound that you seek will ultimately come down to the wood that you choose and the Luthier who builds the guitar. If you are looking for a warmer tone then you would want to lean toward some of the "softer" tonewoods like Mahogany (for the back and sides) and like Sitka Spruce for the top. If a brighter more punchy tone is desired then you would want to lean more toward a brighter "harder" tonewood like we find in the Rosewood family. This is just the first step in building an incredible sounding acoustic guitar. Just choosing the species of wood will not ensure that you get the sound that you want and this is where it gets real..........
Tapping and Listening
Sometimes this is referred to as Tap-Toning and it is the process of tapping and listening to each piece and their tonal properties. This is where the difference between a major guitar manufacturer and goodLuthier begin to part ways. Where a major manufacturer is just going to pull the next top off of the shelf, join it together, sand it to the same thickness as the last one and then move on to the next one with no real regard to sound. A good Luthier (on the other hand) will start by tapping on the wood to determine how and if it will sound good as well as how the tap tone of the top compares to the back and sides. As a builder I have a very good idea as to how a guitar is going to sound based upon tap toning. This comes from years of guitar building experience as well as many years of experience as a tonewood vendor, having re-sawn and listened to several thousand premium guitar tops and back and side sets. I find it very interesting that I can cut 10 guitar tops from the same billet (or piece of wood) and if I am lucky I might find one top that has the tone and look that I seek. Over the years I have collected (and continually improve on) a healthy stash of some of the best guitar tops in the world...... I have sold some of the rest of my stash to many of the most expensive builders in the world ($20,000 +) price range. The best wood I have saved for the guitars that I build.