Stir together the tomatoes, shallot, vinegar, chile flakes, garlic, 1 tablespoon olive oil, 1 tablespoon basil and 3/4 teaspoon salt in a medium bowl. Set aside to marinate, stirring the tomatoes every 10 minutes, while you prepare the spaghetti squash.
Carefully slice off the top and bottom of the squash, trimming just enough so that the inner flesh of the squash is exposed. Use a sharp paring knife to poke ten to twelve 1/2-inch-deep slits all over the squash. Put the squash in to a medium glass heatproof bowl and microwave on high for 5 minutes. Carefully flip the squash over and microwave on high until a fork easily pierces through the flesh that is exposed on the squash, about 5 additional minutes.
Allow the squash to cool enough so that you can handle it, then split it in half length-wise. Use a spoon to scoop out the seeds and discard them. Then use a fork to loosen the squash strands and transfer them to a medium bowl. Add the remaining 2 tablespoons olive oil and 1 teaspoon salt. Use your hands to gently work the oil and salt into the squash. Transfer the squash to a serving platter and pour the tomato mixture over the top (along with all of its juices). Top with spoonfuls of the ricotta and garnish with the remaining basil. Serve warm or at room temperature.
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