I have used cuben and silnylon shelters. To me, the question that would be worth asking yourself is: "When and where do I do the majority of my backpacking?"
In my opinion, the entire choice between shelter materials can be determined in a large measure as to the climate and seasons you go backpacking. Since you live in the lovely Bay Area, I suspect that the Sierra and northern California will be your general backpacking area. If that is the case, and presuming that you don't spend the majority of your time backpacking the wetter sections of the coast (Santa Cruz mountains and far northern reaches of California), then few of the downsides of silnylon really applies, other than the weight penalty over cuben. Silynylon sags in the rain (or areas with high humidity), that much is known and accepted.
In California, I found this isn't much of a consideration, since it barely rains during the summer (again, an assumption that you are a three-season backpacker) and the relatively humidity is very low. You could use just about any well-designed shelter and it would fare well. So then, the entire question becomes one of money, weight and anticipated wear-and-tear. Silnylon is strong, especially in wind. It will put up with a lot. Cuben needs to babied a bit more, as Nick points out.
To some, the weight savings would be worth the money. I prefer cuben here in (often) wet Washington, for the sag factor. But the silnylon tents I've owned were definitively tougher.