Heat the olive oil in a large skillet over medium-high heat until shimmering.
Add the diced onion and sliced poblanos and cook, stirring occasionally, until the onions are caramelized, about 10 minutes.
Stir in the garlic and seeded jalapeños and cook 1 minute more, then add the ground cumin, kosher salt and pepper; stir to combine.
Add the quinoa and cook 2 minutes, stirring to toast slightly, then pour in 2 cups water and bring to a boil.
Cover, reduce heat to low, and simmer until the quinoa is fluffy and water is absorbed, about 20 minutes; remove from heat.
Stir 1 cup of the enchilada sauce into the cooked quinoa, then fold in the drained black beans, chopped cilantro, lime juice, and 1/2 cup shredded cheddar.
Preheat the oven to 350°F (175°C). Pour 1/2 cup of the enchilada sauce into the bottom of a 9x13-inch baking dish.
Wrap the tortillas in a damp towel and microwave for about 1 minute to make them pliable.
Spoon a portion of the quinoa filling down the center of each tortilla, tuck and roll, and place seam-side down in the prepared baking dish.
Pour the remaining enchilada sauce over the filled tortillas and sprinkle with the remaining cheddar and the shredded pepper jack.
Bake for 15–20 minutes, until the cheese is melted and bubbly. Remove from the oven.
Top with sliced avocado, a dollop of yogurt, pomegranate arils, and additional cilantro and serve with lime wedges.