While I had no part in building the site, there's a  relatively accurate general breakdown of time used for building larger websites

http://drupal.org/nyobserver#comment-228767

• 30% Theme (includes significant ajax work)
• 20% Migration
• 25% Data architecture and implementation (CCK+Views)
• 25% Other. Wrangling contrib modules into shape. Writing custom modules.

In most sites the order (in the water fall system which could better for the overall project rather than an agile system which is better for compnents of the site such as design or modules, I personally think a waterfall with each step an agile process could work best) could be

10% base theme

25% Customizing modules/building new modules

10% Data architecture

20% migration

20% Data structure implementation (Views. Building. Some times this step can be mistaken for creating the theme)

25% finalizing the theme to fit in all of the above