Hi Incredible,
Im also interested in what you mean by
"internal linking being as flat as possible and having deep external linking"
Ive not been in forum for a while so if you could give an explanation or put me on to a link I would appreciate it.
When I do a site search in google site:
Businesses for Sale - Buy & Sell Australian Business for Sale it says you have 4080 pages in their index so i would imagine they just see most of the generated pages from your database as duplicate pages. I would imagine most of the listing pages have the same shell to them with very similar information therefore they only show the top level links which are probably 1/2 clicks in from the homepage which is 288 pages.
Im not sure if this is the answer but this is what we see with our jewelry site. The question is, how do you make the pages beyond that fresh with relevant fresh content??