While the squash is roasting, in a large bowl, combine the beans, lentils, and brown rice.
In a sauté pan, heat up the remaining tablespoon of olive oil, and add the mushrooms, onions, garlic, and red bell pepper, and sauté for 15 minutes, until the vegetables are tender and there is no more liquid. Remove from the heat and add the mushroom mixture to the bean mixture.
Season the bean stuffing mixture with cilantro, chipotle in adobo, cumin, ancho chili powder, lime, salt and pepper. As an option, you can add cheese or vegan cheese.
Remove the squash from the oven and adjust the temperature to 350. Fill the acorn squash with the bean mixture and place back in the oven until the filling is warm throughout, about 15-20 minutes. Top with sliced avocado, salsa or additional cheese.