Combine all the marinade ingredients in a bowl large enough to accommodate the squash, peppers, and onions. Mix together well.
Chop of the ends of the delicata, and slice in half around its circumference to make it easier to work with. Slice each half in half again, lengthwise. With a spoon or knife, scoop out the seed and pulp. Place the sliced edge on a work surface so it looks like a tunnel, and slice in ½" curved strips.
Cut the small sweet peppers in half, discard the stem, and remove any seeds and pith. Slice large pieces into smaller pieces.
Remove the papery skin from the red onion, slice off the top and bottom, and cut in half, lengthwise. Slice each half into 6 - 8 wedges.
Place all the vegetables in the marinade and soak on the counter for at least 30 minutes, tossing occasionally.
Preheat the oven to 425 degrees F. Roast the vegetables for 40 minutes on a parchment paper lined baking sheet, or until the red onion starts to caramelize.
Make the quinoa per these directions with a mixture of orange juice and water as the simmering liquid. Measure out 2 cup of cooked quinoa, and toss with the nutmeg. Combine the roasted vegetables with the quinoa on a serving plate, and sprinkle with spiced pepitas and pomegranate seeds.