I really couldn't agree more. He had an opportunity that he seems to have overlooked in favor of his own flavor of partisan hackery. That said, as Stewart himself said, he's not a serious news host, he's a comedian doing a comedy news show. The Daily Show isn't primarily there to deliver news, it's there to be a comedy show. A comedy show on television needs to do exactly two things. It needs to make people laugh, but that's mostly a consideration of genre. The primary purpose is to sell advertising slots to a coherent demographic so they can be targeted by relevant advertisers. Liberal partisan hackery makes a lot of sense when you're trying to target the liberal college students and twenty somethings who make up the show's primary demographic. That may have more to do with Comedy Central than with Jon Stewart, but I'd be surprised if the staunchly liberal stance if the show had nothing at all to do with marketing.
As a comedy show, the Daily Show was excellent. Frequently funny. He and Colbert particularly had a rare chemistry. Unfortunately, it is my opinion that a lot of his viewership watched him to engage in the Yudkowsky sneer club more than they did to be entertained, and certainly more than they did to learn. It is always difficult to draw conclusions about political comedy for this reason.