While the millet cooks, start the chili. In a small bowl, combine the chili powder, cacao powder, cumin, oregano and cinnamon; set the spice mix aside.
In a 10-inch (preferably cast iron) skillet, heat the olive oil over medium-high heat. Add the onions, carrots and celery. Season with salt and pepper. Cook, stirring occasionally, until the veggies are tender, about 5-6 minutes.
Add the zucchini, garlic and another pinch of salt and pepper. Cook, stirring, 2 minutes. Stir in the tomato paste, followed by the spice mix. Cook 1-2 minutes, stirring. Add the tomatoes with their liquid, along with 1 cup of water and the drained pinto beans. Bring to a boil, then reduce the heat to a hearty simmer. Cook 5 minutes.
Remove the pan from the heat and squeeze in the juice from ¼ lime. Taste and season the chili with salt and pepper as needed.
Dollop the millet over the chili and spread it out in a smooth layer. Sprinkle the remaining 1 cup of cheese over the top. Cover with foil and bake 10-20 minutes, or until heated through and bubbling around the edges. Let cool 5 minutes.