Good question.
The portal should really drive your overall page navigation. Remember, the WSF is a sample website showcasing how forms *can* be used - not how they *must* be used. When deploying content to a portal, you will want to ensure that you content is well-structured (XML) and has decent metadata (embedded within the content XML). Portal administrators creating new portal pages can add a portlets to their pages and configure those portlets to query Alfresco to render published content items. But as far as navigation goes, that should be owned by the portal itself, as that is your run-time web app.
To create a portlet easily, you'll want to use our new web scripts in 2.1.0 Community Final. This allows you to write your portlets using Javascript and Freemarker and hook in using a generic JSR-168 compliant portlet container for web scripts. You can look at our out of the box web scripts for our JSR-168 compliant portlets in 2.1.0 Community Final (all using the same generic portlet container). This should give you a good idea of what you can do.
Kevin