Preheat oven to 375 degrees. Brush a large, shallow baking dish with olive oil.
In a large sauté pan, heat olive oil over medium-high heat. Add the onion and cook 8-10 minutes or until beginning to soften and take on a little color.
Add the garlic and cook 1 minute or until fragrant. Add half the thyme and salt and black pepper to taste.
Tilt the skillet, push the onions to one side and drain off any excess oil. Transfer to the prepared baking dish and allow to cool while preparing the vegetables.
Slice the zucchini, tomatoes and potatoes into 1/4-inch slices.
While the vegetables are on your cutting board, season with salt and black pepper.
Sprinkle half of the cheese over the onions.
Starting with the zucchini, place them in the baking dish over the onions, fanning them out into rows.
Next, place the potatoes evenly in between the zucchini followed by the tomato slices. If any vegetables are left, tuck them in wherever you can to use them up.
Once they're arranged, sprinkle with more salt, black pepper and remaining thyme.
Cover the dish with aluminum foil and bake 35-40 minutes or until potatoes are tender.
Uncover the dish, sprinkle the cheese on top, and bake for another 15-20 minutes, or until lightly browned.
Allow to rest 10 minutes before serving.