1. In a saucepan, combine the quinoa with two cups of water and bring to a boil. Reduce heat to a simmer, cover, and cook until all the liquid has been absorbed, about 15 to 20 minutes.
2. Meanwhile, in a wide sauté pan, heat the olive oil over medium heat and sauté the onion until translucent. Add the zucchini, squash, chili pepper, garlic, salt, and pepper. Mix well and cook until just heated through, about four to five minutes.
3. In a heatproof mixing bowl, combine the quinoa and vegetable mixture. Add the paprika, lemon zest, cilantro, and feta cheese and mix well.
4. Preheat oven to 350° F. Lightly oil a 9- x 13-inch baking pan and set aside.
5. Divide the quinoa mixture evenly among the bell peppers, then arrange them in the baking pan. Sprinkle with olive oil, then cover with foil and bake at 350° F until peppers are tender and juicy, about one hour. Transfer to plates and serve.