Apps have one clear advantage. In general, a well-made app can provide a far better user experience than even the best mobile websites are capable of right now. I don't think this is controversial.
Really, though, what I often see missing from such discussions is cost. It's often not that hard to make a web app that will work well on most smartphones (depending on the nature of the app – things like graphics-intensive games being an exception, etc.).
Return on investment should be a question asked when building any application, much less a mobile one. Think of it in terms more than just how many users are going to use it. Remember branding opportunities, and other soft marketing that results before starting.