Cut the theme up in partials, create views for every partial, and optionally use the Theme class to construct a page (more flexible than the template controller).
For our applications we've gone a step further, we have module controllers for every partial in our application, that contain both the logic for that partial and return the partial view.
Our webengine knows (though database definition) what page template to use for a requested URL, which partials are needed for that template, in what section of the template these partials must be added, and what module URI produces the partial. The module URI's are then called using an HMVC call to retrieve the partials and assemble the page.
This allows us to run all our applications of the same web engine and the same base templates and partials (which we use for development). When done the frontend designers can create a bespoke template set for the client using the theme class without needing access to the code.
In my opinion you should put an advanced example of FuelPHP in action on GIT so the newcommers could watch and learn how to do things in Fuel because the documentation doesn't always helps. I personally have been looking multiple solutions for things to be done a good way in Fuel. Such big example would be great to follow "good" practices and learn Fuel awesomeness in action even better.
Many people coming here are mostly asking for 'how to do this and that properly', then you could throw a link so every individual could explore ;)
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