There was a great talk in the Elixir Meetup London by Anthony Pinchbeck about organising functionality not around MVC but the functional unit being build.

So for example if you have something that is dealing with registering your website, create a directory called register_website and all models, functions and controllers to do with that code go in there. The talk suggested deleting the controllers and models directories. He also said there was duplication but everything was more loosely coupled and you could always group things in deeper functional units later.

I'm not 100% brave enough to go for this structure quite yet but it certainly makes coming to a project pretty clear as you literally have a list of all the functions of the site where the code sits for each thing :-)