[eluser]jedd[/eluser]
If I'm parsing your question correctly, one solution is to generate your common view partials in MY_Controller.
Have a read of [url="/wiki/Header_and_Footer_and_Menu_on_every_page_-_jedd/"]this page[/url] and see if that approach would work for you.
I'm not sure at what level of complexity or size it becomes infeasible to do all these potential view partials in MY_Controller. Given most of the grunt work should be happening in your model(s) though, it should be fine.