Start by mixing all the fajita seasoning ingredients in a small bowl. Heat one tablespoon of olive oil in a skillet over medium-high heat. Sauté the onions and garlic for a few minutes, then add the sliced peppers and sprinkle with half the seasoning. Cook until softened, then remove from heat.
Using a sharp knife, slice a pocket lengthwise into each chicken breast without cutting all the way through. Rub the remaining seasoning all over the chicken. Spoon the cooked peppers and onions into each pocket and add shredded cheese. Use toothpicks to secure the openings so the filling stays inside.
Heat the remaining olive oil in the same skillet and place the stuffed breasts in the pan. Sear for a few minutes on each side until golden brown. Add a splash of water, cover the skillet, and let the chicken cook on low until the inside is fully done. Remove the toothpicks, garnish with parsley, and serve with lime wedges.