Bring first 4 ingredients and water to cover to a boil in a saucepan over medium-high heat; reduce heat to medium, and simmer, stirring occasionally, 20 minutes or until beans are tender. Drain beans, reserving 3/4 cup cooking liquid. Discard yellow onion, thyme, and garlic.
Cook bacon in a large skillet over medium heat 7 minutes or until crisp, turning once. Remove bacon, reserving 2 Tbsp. drippings in skillet. Drain bacon on paper towels, and crumble.
Sauté chopped sweet onion in hot drippings over medium-high heat 5 minutes. Stir in corn, and cook, stirring often, 6 minutes or until corn is tender. Stir in tomatoes, cooked lima beans, and 3/4 cup reserved cooking liquid; cook, stirring occasionally, 5 minutes. Stir in butter and next 3 ingredients. Season with salt and pepper. Sprinkle with crumbled bacon.