I\'m having a nightmare trying to get a simple installer working in InstallShield LE (the one shipped with VS 2012). There are all kinds of problems that I can work around (like
Each setup tool has its problems. Please note that there are no tools which can accurately detect your application dependencies. The best a tool can do is make suggestions. This is why most setup developers determine the dependencies themselves and manually include them in the installer.
If you're not happy with InstallShield, you can try a different setup tool: http://en.wikipedia.org/wiki/List_of_installation_software
The free version of Advanced Installer includes a Visual Studio setup project which may help.