Did you guys looked at Modular Extensions?
http://codeigniter.com/wiki/Modular_Extensions_-_HMVC/
All about this issue was studied and many different approaches were taken into account before we get to the actual version of Modular Extensions and what it is capable of. To better understand it, take a look into the threads about modules in CodeIgniter:
I did start to ask about the best way to structure my application here:
http://ellislab.com/forums/viewthread/68847/
And we had other parallel discussions about the same theme:
http://ellislab.com/forums/viewthread/64087/
http://ellislab.com/forums/viewthread/71506/
http://ellislab.com/forums/viewthread/73899/
But the discussion about NESTED MVC started to ignite here:
http://ellislab.com/forums/viewthread/70425/
(I was arguing there why Libraries, Helpers, Plug-ins and Models are not suited for modular needs)
Then born the first version of Modular Extensions:
http://ellislab.com/forums/viewthread/71940/
And soon after, the second version:
http://ellislab.com/forums/viewthread/72123/
And the third version…
http://ellislab.com/forums/viewthread/72580/
Finally, the fourth and last version:
http://ellislab.com/forums/viewthread/73177/
We have some modules examples:
http://ellislab.com/forums/viewthread/73401/
And discussion about what is best:
http://ellislab.com/forums/viewthread/73312/
Modular Extensions is powerful, elegant, well done, very flexible, and solves any problem about modular needs in CI, including a complete HMVC or just for View partials. It was made based in the CI core, so it follows the CI standards, without hacking the core.
With it you can organize your code into separate folders, to write your own plug-and-play modules. But also, it allows you to load how many nested modules you want. The modules are very close to Controllers, so it is the best approach to the HMVC concept.
You can have only one controller for the public part of your application and modularize everything else in your application, if you want. There are many things you can do with it, in many possible ways. It is up to your imagination. Also, new features will come soon.