Place the quinoa in a small pot with 1½ cups water. Bring to a boil, then lower to a simmer, cover and cook for 14-15 minutes until all the liquid has been absorbed. Let the quinoa rest for 5 minutes, covered, then fluff with a fork.
While the quinoa is cooking, place the eggplant in a colander and sprinkle with 1 teaspoon kosher salt. Set aside for 15-20 minutes while you prep the other vegetables. Place the eggplant between two layers of paper towels and thoroughly pat it dry. Set aside until ready to use.
Pre-heat your oven to 375 degrees.
Heat a tablespoon of olive oil in a large non-stick pan over medium-high heat. When hot, add the onion, bell pepper, garlic and a pinch of kosher salt. Cook for 5-6 minutes until the onions become translucent and the bell peppers have softened slightly. (Be careful not to burn the garlic, peeps! If it starts to brown, turn down the heat a little bit.) Add the zucchini and eggplant and cook for 5 minutes until just tender. Stir in the tomatoes. Reduce the heat to medium-low, cover, and cook for 15 minutes until the vegetables are soft (but not mushy!) and the tomatoes have broken down.
Turn off the heat and stir in the quinoa, pesto and mozzarella. Taste and season generously with kosher salt and fresh ground pepper. If you like a kick, feel free to get some crushed red pepper involved. (Please make sure this awesomeness is very well seasoned, capiche? I’d give you specific quantities of salt and pepper, but it will vary based on your pesto and the salt content of your mozzarella.)
In a small bowl combine the Panko, Parmesan, and crushed red pepper.
Transfer the filling to a medium baking dish (I used a 12-inch ceramic dish) and top with the Panko mix. Bake for 30 minutes until the top is golden brown and the cheese is bubbling up around the sides.
Let your quinoa bake cool for 10 minutes before serving. (I recommend serving this with extra pesto or freshly chopped basil, but you do you.)