Well, if you're going to go there, then A Clockwork Orange and 2001: A Space Odyssey. One can easily complain that Anthony Burgess wrote a better book filled with imagery and politics (and a glossary!) which Kubrick failed to capture, so that one might be arguable. On the other hand, while Arthur C. Clarke wrote a good book that Kubrick largely ignored, the result was one of the most innovative films in history. The film brought space to life in a way that printed words could not. Sure, Kubrick's work can now be easily CGI-ed up, but he thought to do all of it and he did it the hard way before we had computers.

As far as Eyes Wide Shut goes... I kinda hated it because it felt like the default daydream of old men fantasizing about what they wish they'd done back when they couild still get it up. I read an article years ago about how for years Kubrick had script readers who would read hundreds of books and scripts to give him recommendations for what to make into his his next movie and they were all terrified of recommending something beneath The Master, and then he didn't like the things he did see, and this went on and on, and I feel like he was stuck with material that a concensus would find acceptable/interesting rather than anything that was more avant garde.