[eluser]kurucu[/eluser]
I don't wish to be hated, but if it is just an intranet you are developing (i.e. clever content) then ModX might be a good place to look, especially the Revolution version (currently in beta phase) which allows you to specify different 'contexts' e.g. for your university microsites. It is very powerful and through the use of 'snippets' allows you to generate and present content from an unlimited variety of sources.
Hatespeach over.
In my mind, controllers are normally broken into functionality rather than necessarily site areas. That said, you can of course do what you want. However, by ordering them by functionality only the resources needed for each function have to be loaded and so they are more efficient. Also, it's cleaner and simpler to follow (you would pass a parameters to change context). You can store them in folders, and this does the same as on disk - for categorisation and organisation.
With CI (and probably any framework/cms) you have to stop thinking of the raw filesystem unless debugging. Instead, you have to think in terms of the frameworks native language and intentions, otherwise there is probably going to be a collision later down the line, or maybe even no point to using the framework.
So, thinking in CI terms, it's obviously worth reading the documentation, but the controllers are essentially the request brokers, pulling in the relevant data, processing it, and sending it off to somewhere for changing to a suitable output. Despite the fact that they are stored on the filesystem, you rather want to forget that users could access any other resource except images/client scripts/css etc.
There are many deviations and advanced/specific uses of controllers and folders in the controller directory, but that should be enough to get you thinking.
