I agree that some directories will become trusted sources and the vast majority of directories built as link farms will become useless to webmasters and fade from existence. The internet is constantly evolving and the serious directory operator must keep up with the ever changing environment. Directories have been around long before search engines and the quality directory will in my opinion always have a vital role on the internet.
A good directory must work with search engines as a trusted source for quality human reviewed content. When you have put years of development into a directory and get search engine concentrations of millions of pages you have a strong marketing tool for the webmaster and a great deal of traffic from organic searches. The major error I see with a lot of well intended directories is not developing the vital search engine concentration that will be necessary to survive.