I have come to believe that tires and wheels are the first decision in a bike purchase. Tires and wheels have a big impact on how you can use a bike and how it will ride. Because of this the best upgrade is often tires and or wheels.
From what type of bike, mountain, cyclocross, rough road, smooth road or track. Tires and wheel size will determine a lot of the fork and fame design. It should be the first decision made when deciding on a custom bike and one that cannot be easily upgraded later.