Because the "site:" operator does not rank on popularity or PR. I think it never has, and if it did, it was changed a long time ago. It merely shows you the indexed pages for a site. You can still gather a little info from it to see, for example, which pages are likely to appear in the secondary index / supplemental results ("In order to show you the most relevant results, we have omitted some entries"). Pages in index is somewhat of a vanity metric. It can be more insightful to look at the number of pages that send you at least 1 visitor a month.
If Google would rank "site:" on popularity people would probably (ab)use it for icky stuff like PageRank sculpting or figuring out how (internal and external) linking influences ranking, much like they did with popular search words /trends.
In the same vein "Link:" does not show all pages that link to a site and doesn't order them by link strength.
If you want more reliable information on links and page importance set up webmaster tools and analytics.