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I have 4 main top-level categories from the homepage, let's call them A, B, & C. I'm going to use A as an example:
Within A are 15 or so subcategories. Each one of these subcategories targets a keyword phrase. Usually, the keyword phrase is a derivative of one of the main keywords that the homepage targets (e.g. "dogs" and "golden retriever dogs"). Within each subcategory there are further subcategories which are, usually, not targeting keyword phrases in and of themselves, but are re-enforcing the keyword phrase being targeted in the level before it (e.g. "dogs", "golden retriever dogs", "golden retriever dog pictures"). Then, the 4th level are all content pages which don't really target any keyword phrases, but might have them in the text somewhere (so it would re-enforce the cats/subcats before it). I cross link pages within a level (except I don't cross link content pages) (e.g. I cross-link all the subcategories within category A).
The site is informational in nature, and I plan on having thousands of content pages. If I trade reciprocal links, I plan on having a separate links page for each category/subcategory. I want to get ranked for the main keywords, as well as the keyword phrases. I don't just want an all-star homepage getting just the main keywords. I want that, as well as, having my cat/subcat pages come up for specific keyword phrases.
Too often I see people trying to 'pack in' their keywords, all in the title, headlines, and content on the home page - when they should use the home page for the primary keyword(s), then have a link menu out to their subpages to handle the many secondary keywords (title/headlines/content, etc).
In my experience on dozens of our sites, a subpage will be indexed by Google as fast and as effective as the home page. Often, if a news story breaks, we can add a subpage with a prominent news title and content, and Google will track the story from the home page, to the subpage, and list the subpage story on page 1 of the SERPs the next morning.
I always try to (fairly) closely match the link title on the home page to the page title of the subpage, though, which I believe adds a little additional validation for Google.
Looks like you'll have a winner.