Preheat the oven to 350°F.
Heat 2 tablespoons extra virgin olive oil in a large skillet over medium-high heat. When the oil shimmers, add the diced sweet onion and sliced poblano peppers. Cook, stirring occasionally, until the onions are caramelized and the poblanos are softened, about 10 minutes.
Add the minced or grated garlic and the seeded, diced jalapeños; cook, stirring, for 1 minute. Stir in 2 teaspoons ground cumin and 1 teaspoon kosher salt and pepper, then add 1 cup quinoa and cook, stirring, for 2 minutes.
Pour in 2 cups water, bring to a boil, cover, reduce the heat to low, and simmer until the quinoa is fluffy and the liquid is absorbed, about 20 minutes. Remove from the heat and fluff the quinoa with a fork.
Stir into the cooked quinoa: 1 cup red enchilada sauce, the drained and rinsed 14-ounce can black beans, 1/2 cup chopped fresh cilantro, the juice of 1 lime, and 1/2 cup shredded cheddar. Mix until combined.
Pour 1/2 cup of the red enchilada sauce into the bottom of a 9x13-inch baking dish. Wrap the tortillas in a damp paper towel and microwave for 1 minute (warm in batches if needed to keep them pliable). Spoon some of the quinoa–bean mixture down the center of each tortilla (enough to roll without overfilling), tuck the ends, and roll. Place each rolled tortilla seam-side down in the prepared baking dish.
Pour the remaining enchilada sauce evenly over the rolled enchiladas. Sprinkle the remaining 1/2 cup shredded cheddar and the 1/2 cup shredded pepper jack over the top.
Bake uncovered for 15–20 minutes, until the cheese is melted and the sauce is hot and bubbly.
Remove from the oven and top with sliced avocado, yogurt, pomegranate arils, and additional chopped cilantro. Serve with lime wedges.