Why would the number of pages make a difference? There aren't two sets of guidelines for what constitutes effective optimization, one for sites with fewer than a million pages and the other for sites with over a million.
Of course, with that many pages, you're going to have to rely on templates and almost certainly at least some kind of automation. I find it hard to think how you would manage over a million pages and all the data and transactions they would generate, all by hand. What specifically you would do -- what specifically you CAN do -- would depend on the available technology and resources, the existing site structure and what exactly you're trying to accomplish. "Optimization" is way too vague a term to serve as a real goal.
Surely with that large a site, the organization in question would be able to hire a professional SEO who could answer these sorts of questions and come up with a viable plan?