Position a rack in the center of the oven and preheat the oven to 375°F. In a small bowl, mix together the cereal, agave, lemon zest, cinnamon and nutmeg.
Using a melon baller, scoop out the apple cores. Place the apples cut side up in a large ovenproof skillet. If necessary, cut a small slice off the bottoms of the apple halves to keep them from toppling over. Sprinkle 1 tablespoon of the brown sugar over the apples. Fill the apple cavities with the cereal mixture then mound the mixture generously on top of the apples, allowing it to nearly cover the entire cut surface of the apples.
Pour the apple juice into the bottom of the skillet and place the skillet in the oven, lightly covered with foil. Bake the apples for 20 minutes, then remove foil and bake until they are crisp-tender and the stuffing is golden brown, about 20 minutes more.
Transfer the apples to plates. Add the remaining 1 tablespoon of brown sugar to the cooking liquid in the pan and simmer over medium-high heat until it thickens slightly, about 5 minutes. Stir in the lemon juice.
Spoon the sauce over the hot apples and serve each with a dollop of yogurt.