Have someone who has never heard of the design project critique it extensively. For large projects, a review at the concept stage is important too. The Prototype PCB Lay out a through-hole PCB for the prototype. If you use hand-wired boards you will spend more money fighting with them than the PCB would have cost, and the resulting PCB is still likely to need a respin. Begin by examining the net list.
Grounds can have similar problems.
Place all IC's parallel to the board edges, with pin 1 on the left, so that you can easily read the labels on horizontal IC's. Place all other identified pin 1's, especially connectors, consistently. Mark every pin 1 with a square pad. Connect the spares' pins with traces that will be easy to cut. If possible, add connection points that meet your company standards for manufacturing rework.