Hmmm...that's a tough question.

I would say a custom bike is the best thing in the world, but if this is your first bike, I'm afraid about you not know exactly what you like, and possibly wasting a whole bunch of money. A fit system can only do so much, after that, there is personal preferance that plays a part in fit. For example, I love being stretched out on a bike. My DH couldn't believe I wanted a slightly longer stem on my mountain bike, but I love feeling stretched out. A good friend of mine is completely opposite. He likes a frame a little small and feeling tighter on a frame. Totally personal preference that I really don't think a fit system could capture.

If you have some time on a bike and have an idea of what you like/don't like, I would say go for it!!!

Another option could be to purchase a nice frame (not custom) and then work with a shop to create a custom build to fit your needs.