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1
Adjust oven rack to upper-middle position and heat oven to 400 degree. Brush 13- by 9-inch baking dish with 1 teaspoon oil; set aside.
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2
Toss zucchini and squash slices with 1 teaspon salt in large bowl; transfer to colander set over bowl. Let stand until zuccchini and squash release at least 3 tablespoons of liquid, about 45 minutes. Arrange slices on triple layer paper towels; cover with another triple layer paper towels and firmly press each slice to remove as much liquid as possible.
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3
Meanwhile, place tomato slices in single layer on double layer paper towels and sprinkle evenly with 1/2 teaspoon salt; let stand 30 minutes. Place second doube layer paper towels on top of tomatoes and press firmly to dry.
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4
Meanwhile, heat 1 teaspoon oil in 12-inch non-stick skillet over medium heat until shimmering. Add onions, remaining 1/2 teaspoon salt, and 1/4 teaspoon pepper; cook, stirring occasionally, until onions are softened and dark golden brown, 20 to 25 minutes. Set aside.
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5
Combine garlic, 2 teaspoons oil, remaining 1/2 teaspoon pepper and thyme in small bowl. In large bowl, toss zucchini and squash in half of oil mixture, then arrange in greased baking dish. Arrange caramelized onions in even layer over squash. Slightly overlap tomato slices in single layer on top of onions, Spoon remaining garlic-oil mixture evenly over tomatoes. Bake until vegetables are tender and tomatoes are starting to brown on edges, 40-45 minutes.
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6
Meanwhile, process bread in food processor or belender until finely ground (about 10 seconds). You should have about 1 cup crumbs. Combine bread crumbs, remaining teaspoon oil, parmesan and shallots in medium bowl. Remove baking dish from oven and increase heat to 450 degrees. Sprinkle bread crumb mixture evenly on top of tomatoes. Bake until bubbling and cheese is lightly browned, 5-10 minutes. Sprinkle with basil and let sit at room temperature 10 minutes before serving.
