Site with about 3000 real pages and infinite Duplicate Content issues (unchecked wildcard parts of URLs) that were fixed at the beginning of the year shows 100 000 URLs "ever crawled" (sounds reasonable) and the "indexed" count is just over 8000.
However, for the last 18 months, the site: search only ever returns between 700 and 750 URLs. Even during and after the mass redirecting of the old multiple-parameter URLs and old .html (rewritten) URLs to the new single extensionless URL per page, the numbers in the site: search did not go up.
In WMT internal linking reports, many of the listed pages were showing upwards of 50 000 internal links at the start of the year, and that figure is now down around the 8000 mark. This figure is over-reported and the simple reason for that is Google hasn't yet crawled all of the redirects from old to new URLs so believe the old URLs still exist and are still counting the links that used to exist on those pages.
So it seems that the WMT "indexed" figure relates to "URLs that link to each other within the site".
However, with 8000 URLs reported as "indexed" in WMT there's still only 730-ish URLs showing for the site: search.
At site relaunch, the old 3000 page site had about 500 new pages added (extensionless URLs), and a few hundred old pages (parameterised or .html URLs) went 404. All old content pages (both .html and parameterised) that still exist have redirects from those old URLs to the new extensionless URL for the page. Requesting one of the pages that are now retired returns 404 at the requested URL, and if you ask again you get 410 Gone every time after.
With crawling at a very minimal number of pages per day (under 450), it looks like the site is under some sort of crawl-budget penalty. Crawl rate was over 3000 URLs per day for a while after the relaunch, but with flat-topping on the graph indicating some sort of enforced limit? Maybe 80 000 redirects from the old duplicate content riddled URL structure to the new extensionless structure was a bit much for the old Googlebot to handle? The site was offline for a couple of hours about a week apart at one point, and immediately after the second event crawl rate dropped to under 500 URLs per day and has stayed there.
[edited by: g1smd at 2:45 pm (utc) on Jul 25, 2012]