Hi and Welcome,
I believe that one major factor when going supplemental with many pages is the lack of uniqueness in pages.
Rendering a dynamic site from a big database often makes it easy to generate templated pages, those pages often seem too similar to the bot.
my 2c:
Choose a main KW or two for each page.
- URL – use one Unique URL per page, Keep it under 2 parameters, avoid session id or any structure with an outcome of visibly duplicate content, preferably use KW e.g.: domain.com/KW
- Title - Every page deserves a unique title starting with its KW.
- Keyword tag - don't use the same tag all across the site, empty is better.
- Description tag - don't use the same tag all across the site, empty is better.
- Content - unique content on each page/URL, preferably at the top of the source.
- Anchor - Use the relevant KW while linking to a page, this could be done using the link's anchor or alt/title attributes.
- Links (In-site links) - Build proper archives, sitemaps and navigation, some supplemental results are pages that had visible strong links and became orphan (this is common with content that used to have a link from the homepage and the webmaster replaced/removed it).
- Links (Incoming ones) - non homepage deep links never hurt.