Thanks for you answer Ryan.
I should specify a bit more the purpose of the site. It will aggregate stories created on regional newspapers. The inter-regional part will be managed by an editor who will choose the stories that will show up. Same thing on the regional level.
The problem comes from the dual navigation. We want to allow people to navigation on a higher lever instead of forcing them to be on the regional level as soon as they click a link.
Example:
You are on Western US page because you are interested in what happen in this region. You find an interesting article written by a local newspaper in California.
If we send him to the regional version of the article all the navigation will switch the a regional navigation. Meaning that all the categorie links (like politics) will send him to a list of California politics articles instead of sending him to the Western US politics section.
Am I clear in my explanations?
I'm thinking a cookie based navigation could work but again not sure about the SEO friendlyness of this technique.