It is important to understand project types:
If you have a generic application to deploy, use Generic Application Template, otherwise you need to choose one of Metatrader templates for your needs. Metatrader templates display Metatrader directory structure to select, Generic Application does not. Even if you have choosen Metatrader template and did not put any Metatrader content, this would make your directory structure (template) same as Generic.
As you see it is all about Directory Templates applied at the end. For now there is no way to change Project Type after having created the project, choose your project template wisely. If you are not Metatrader developer, pick Generic Template, otherwise you choose one of Metatrader templates.