For me, it comes down to getting the specs you want. I love thick necks - tried out everything in local stores for months and months and never found one. In fact, they all seemed like the same guitar in different colors. Decided to build my own and one call to USACG solved all of my problems. The customs I've played are just night and day compared to the off the rack guitars. Peruse the galleries of boutique builders - very few guitars that remotely resemble what's in the stores and for good reason. I agree that cost is an issue as we'll as resell. But, many times, the guys complaining about cost are the guys buying an $800 guitar, then spending another $600-800 modding it and trying out various pickups, only to find they still don't have the guitar they really want.