Preheat the oven to 425°. In a large, deep ovenproof skillet, melt 3 tablespoons of the butter in the oil. Add the shallots and thyme, season with salt and pepper and cook over high heat for 1 minute. Cover tightly and roast for about 30 minutes, until very tender.
Meanwhile, in a large saucepan of salted water, cook the limas until just tender, 5 minutes. Drain and cool under running water. Spread on paper towels and pat dry.
Transfer the shallots and thyme to a plate; leave as much fat in the pan as possible. Lower the oven to 375°. Strip the thyme leaves from the sprigs and return to the shallots. Add the flour to the skillet and cook over moderately high heat, whisking, for 1 minute. Add the half-and-half and simmer until thickened, 5 minutes. Remove from the heat. Stir in the limas, shallots, thyme and tomatoes; season with salt and pepper. Spoon into six 1 1/2-cup ramekins and set on a baking sheet.
In a bowl, toss the panko and parsley with the 1 tablespoon of melted butter; sprinkle over the gratins. Bake for 30 minutes, until bubbling. Turn on the broiler and broil for 2 minutes, just until browned. Let the gratins rest for 10 minutes before serving.