Preheat the oven to 425°F (220°C). Cut the eggplants in half lengthwise, score the flesh in a crosshatch pattern without cutting through the skin, and place them cut-side up on a rimmed baking sheet.
Drizzle the eggplant halves with 2 tablespoons olive oil and season with ¼ teaspoon salt and ¼ teaspoon black pepper. Roast for 30–35 minutes, until the flesh is completely tender.
Remove the eggplants from the oven and cool until easy to handle. Scoop out the flesh, leaving about ¼ inch attached to the skins, then roughly chop the roasted flesh.
Spread 1 cup tomato sauce over the bottom of a large baking dish and arrange the empty eggplant shells cut-side up over the sauce.
Heat 1 tablespoon olive oil in a skillet over medium heat. Add the diced onion and cook for 4–5 minutes until softened. Add the minced garlic and cook for 30–60 seconds until fragrant.
Add the diced tomatoes, chopped roasted eggplant flesh, oregano, red pepper flakes, remaining ½ teaspoon salt, and remaining ¼ teaspoon black pepper. Cook for 5–7 minutes, stirring occasionally, until the mixture is cohesive and excess moisture has cooked away.
Remove the skillet from the heat and cool the mixture for about 5 minutes. Transfer it to a mixing bowl and stir in the breadcrumbs, feta, egg, parsley, and basil until evenly combined.
Reduce the oven temperature to 400°F (205°C). Spoon the filling evenly into the eggplant shells, gently mounding the filling without packing it down.
Bake the stuffed eggplant for 20–25 minutes, until heated through and lightly golden on top. Broil for 1–2 minutes at the end if a more browned topping is desired, watching carefully.
Rest the stuffed eggplant for 5 minutes, then drizzle with fresh lemon juice and garnish with additional parsley and basil before serving.