Set a large 12-inch saute pan over medium heat and add the olive oil. Once hot, add the onions and garlic to the pan. Cook the onions, stirring occasionally, until they are wilted and lightly caramelized, about 5 to 7 minutes. Add the eggplant and thyme to the pan and continue to cook, stirring occasionally, until the eggplant is partially cooked, about 5 minutes. Add the green and red peppers, zucchini, and squash and continue to cook for an additional 5 minutes. Add the tomatoes, basil, parsley, and salt and pepper, to taste, and cook for a final 5 minutes. Stir well to blend and serve either hot or at room temperature.