There are a whole lot of things you can't do with ClickOnce applications, like install a shortcut to the user's desktop or have any sayso in where the application gets installed. For some people these are dealbreakers.
Also it's been a while since I used it, but there's a special way you can use to figure out and display the ClickOnce version/build number, which is separate from the application's version/build number. You have to do a try/catch and if the ClickOnce version/build number throws an exception then the application is not running as a ClickOnce-deployed application (that is, it's running as a regularly compiled application or from Visual Studio).
For an application which is simple (that is, not Microsoft Word, but rather a quick-and-dirty application to do something) and needs a lot of regular deployment, ClickOnce is great. But you rather quickly hit the wall of "oh, this can't be done by ClickOnce, please choose MSI or something else).