Microsoft Office Project Server 2003 provides an excellent basis for building on, and many higher-end corporate business scenarios can be fulfilled using the functionality inherent in Project Server 2003 in combination with third-party applications and project partner expertise.
Check out the third-party add-ins available in the market prior to beginning any Project Server customization because the solution you are looking for may already exist.
When addressing problem areas in your organization, first examine whether these problems are going to be fixed by implementing a process or whether they relate more to a technology issue; this will help you find the ultimate solution.
Take time to analyze the needs of your organization to find the appropriate third-party or other solution.