Preheat oven to 400°F (200°C). Line a baking sheet with parchment paper.
Brush the cut sides of the halved eggplants with 2 tablespoons of olive oil. Place them cut-side down on the baking sheet and roast for 25–30 minutes until the flesh is tender.
Remove the eggplants from the oven and let them cool slightly. Carefully scoop out most of the flesh, leaving a ½-inch shell. Chop the scooped-out flesh and set aside.
Heat the remaining olive oil in a skillet over medium heat. Sauté the onions for 5–7 minutes until soft. Add garlic and cook for 1 minute. Stir in the chopped eggplant, tomatoes, salt, pepper, and red pepper flakes. Cook until tomatoes soften, about 5 minutes. Remove from heat and stir in breadcrumbs, herbs, and half the cheese.
Turn the eggplant shells cut-side up on the baking sheet. Fill each with the vegetable mixture. Sprinkle the remaining cheese on top.
Return the stuffed eggplants to the oven and bake for 15–20 minutes, until heated through and the cheese is golden and bubbly.
Garnish with extra herbs or a drizzle of olive oil and serve warm.