First, chop the eggplant, zucchini, tomatoes, and bell pepper into uniform 1-inch (3 cm) pieces. This ensures everything cooks evenly. Finely chop the onion and mince the garlic.
In a large skillet or Dutch oven, heat the olive oil over medium heat. Add the chopped onion and cook for 4-5 minutes, stirring occasionally, until it becomes soft and translucent.
Add the minced garlic and eggplant to the skillet. Stir well to coat the eggplant in the oil and cook for 3-4 minutes. The eggplant will begin to soften and absorb the flavors from the onion and garlic.
Pour in the red wine or vegetable broth to deglaze the pan, scraping up any browned bits from the bottom. Stir in the paprika, smoked paprika, red pepper flakes, ginger, oregano, salt, and brown sugar. Allow this mixture to simmer on low-medium heat for about 5-6 minutes, letting the flavors meld together.
Add the chopped zucchini, bell pepper, and tomatoes to the skillet. Stir everything together gently, ensuring all the vegetables are coated in the sauce. Let the mixture simmer for 10-15 minutes, or until the vegetables are tender but still hold their shape. Avoid over-stirring, which can cause the vegetables to break down.
Stir in the tomato paste until it is fully incorporated, followed by the balsamic vinegar. This final addition will brighten the entire dish. Cook for one more minute.
Taste the ratatouille and adjust the seasoning with more salt and pepper if needed. Garnish generously with fresh thyme before serving. For the best flavor, let it rest for about 15 minutes before serving to allow the flavors to mingle.