Preheat the oven to 190 degrees C. Put an ovenproof dish, preferably metal and measuring about 30 × 20 × 4 cm, in the oven and allow it to heat for 10 minutes. Combine the onions and sweet potatoes in a bowl, drizzle with 1 tablespoon of the oil and gently toss to coat. Tip into the heated dish and roast for 30 minutes, turning the vegetables after 15 minutes.
Blend the remaining oil with the garlic and 1 teaspoon of the thyme in the bowl. Add the zucchini, mushrooms and tomatoes, and gently toss to coat. Tip into the dish and roast for a further 20 minutes.
Meanwhile, put the flour in a bowl and rub in the butter using your finger-tips. Add the water and mix together with a fork to make large crumbs. Stir in the breadcrumbs, cheese, nuts, seeds, pepitas and remaining thyme.
Sprinkle the crumble mixture over the vegetables. Bake for 15–20 minutes until the topping is golden brown and all the vegetables are tender. Remove from the oven and leave to stand for 3–4 minutes before serving.