A dealer will always want to sell you what they have, just because it's a sale 'now' versus a sale 2 months from now. That being said, a vehicle is a huge investment (for most people), hence you typically want to get exactly what you want. It's entirely up to you at that point whether or not people what the dealer has in stock is good for you. In my case, I wanted an SLT1, but with a 4cyl w/ AWD, and to make things worse - merlot color (red) - a pretty uncommon config. I decided to factory order, because for me, this will be a vehicle that I will be sticking with until it can't run anymore. If I'm going to drop $30K on a vehicle, it should be exactly what I want.
On average, you'll note that most people here have waited around 8 weeks for a factory order to be delivered. Some people have gotten them a little sooner (6 weeks), and some a little longer (11-12 weeks), depending on dealer allotment and build schedule. As NY_Joe mentioned, you also risk loosing potential incentives or financing rates. But that comes down to you signing off on a good price when they order the vehicle. But it's a new vehicle in very high demand, so the dealer isn't going to drop their pants.