Heat 3 tablespoons olive oil in a large nonstick pan over medium heat. Add eggplant with 1/4 teaspoon salt and cook, stirring frequently, for 10 to 12 minutes until soft and browned. Transfer to a plate.

Add 1 tablespoon oil to the pan. Cook zucchini for 3 to 4 minutes until tender-crisp. Season with 1/4 teaspoon salt and transfer to a plate.

Add remaining 2 tablespoons oil. Sauté onion and bell pepper for 5 minutes, then add garlic and cook 3 minutes more without letting it brown.

Add tomatoes with their juices, tomato paste, thyme, sugar, red pepper flakes, and 3/4 teaspoon salt. Cook 8 to 10 minutes until the tomatoes break down into a sauce.

Return the eggplant to the pan and bring to a gentle boil. Reduce heat and simmer uncovered for 10 minutes until the eggplant is very tender.

Add the zucchini and cook 1 to 2 minutes until warmed through. Taste and adjust seasoning. Sprinkle with fresh basil and thyme, drizzle with olive oil, and serve warm or chilled.