Update Jan 2017 - Guillermo del Toro and Dreamworks recently released Trollhunters on Netflix which features a gemstone city so this idea has been "done." On to the next!
I would like to see a short film or feature animation set entirely in a cave or other deep netherworld of the earth. Visually it could be stunning. (Think gemstone cities). First story idea I thought of was “What if a bat wasn’t born blind? What if he could see and none of his friends could?”