When I read these requirements I tend to agree with Yannick. (first advise)Hi Rob,
WebCenter Portal seems the one to use.
However, when you add the requirement to easily 'create' an application with different pages etc. Spaces might be a better fit.
In Spaces you can (re)create a completely different UI as well.
It will give you the flexibility to create a different app quite easily.
If you want to stick to WebCenter Portal, you could create a set of pages with navigations etc.
Depending on the role of the user you could grant him access to pages or the entire 'application'
The pages.xml controls the security.
You need to create a navigation.
The navigation can include the pages.xml, but you don't want that. :)