I assume by builder you mean a general contractor?
I would first start out by asking what aspects he will directly be handling in the build if anything at all. I would then ask about his subcontractors and how long he has had relationships with them. If one of them is working through reputable companies in the area versus one guy with a crew of day labor, that should tell you which crew to do with. It seems to me most GC sub out a lot of work. So its best to know who is actually doing the work for you in your home.
One random thought, make sure you are using time tested products and subs. My parents have very noisy plumbing because the sub used an odd mounting bracket for the pipes instead of tried and true methods. Another though, stay away from first gen tech, especially if its in walls. For instance when PEX first came out there were a lot of issues with pinhole leaks and bad fittings.
Has it been suggested to wire everything and anything you might need with network cable and coax? You might check with your electrical sub, but this could be something you could do and it would save a crap load. But check with the contractor because i've heard of it being a code issue or instances of d-bag subs who cuts lines because they didn't install them.
