I agree with a lot of what's already been said. I will add a few things:
Do your homework on the luthier you select. Try to play his/her guitars. Most luthiers have a tone they tend to go for, and there is no substitute for playing more than one of the luthier's guitars to get a sense of that tone. If you can't, there are often videos on YouTube, or on Dream Guitars and Guitar Gallery's website that may help you get a sense for tone.
Ask around. The AGF is a wonderful place to talk to people about the guitars they have commissioned from the same luthiers. People are very honest when you PM them.
After tone, neck profile and nut width will determine how playable the guitar is. One of the best aspects of a customer build is the ability to find a luthier who can make a great "fit" that makes the guitar as comfortable and easy as possible for you to play in your style.
Good luck!
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