This is a wonderful warm side dish that can be easily personalized with your favorite flavored or unflavored olive oil. Serve as a side with a delicious roasted chicken or by itself over rice or quinoa for a vegetarian meal.
Preheat the oven to 375 degrees. Brush a 9 x 13 x 2-inch baking dish with olive oil. In a medium sauté pan, heat 2 tablespoons of olive oil and cook the onions over medium-low heat for 8 to 10 minutes, until translucent.
Add the garlic and cook for another minute. Spread the onion mixture on the bottom of the baking dish. Slice the potatoes, zucchini, and tomatoes in 1/4-inch-thick slices. Place them alternately in the dish on top of the onions, as tight as possible in a single layer. Sprinkle with salt, pepper, thyme and drizzle with 2 more tablespoons of olive oil.
Cover the dish with aluminum foil and bake for 30 to 40 minutes, until the potatoes are tender.
Uncover the dish, sprinkle the cheese on top, and bake for another 20 to 30 minutes, or until browned. Serve warm.