1. Trim zucchinis and cut in half lengthwise. Using a spoon, carefully scoop out the zucchini pulp leaving the shells about 1/4 inch thick and set aside.
2. Roughly chop zucchini pulp.
3. Saute onions, pepper, and garlic in the olive oil until the onions are tender and translucent, about 5 minutes.
4. Add zucchini pulp and pecans and continue to saute about 3 minutes.
5. Add tomato, rice, thyme, salt and pepper, and stir gently to combine all the ingredients.
6. Stuff reserved zucchini halves with rice mixture and top with the mozzarella and parmesan cheeses.
7. Place zucchinis in a small, shallow casserole dish and cover with aluminum foil.
8. Bake at 350 degrees for 30 minutes.
9. Remove foil, and return to oven for about 10 minutes, or until tops are lightly browned and bubbly.