Preheat oven to 375°.
Cook lima beans in boiling water 5 minutes or until crisp-tender; drain.
Cook bacon in a large nonstick skillet over medium heat until crisp. Remove bacon from pan, reserving 2 teaspoons drippings in pan. Crumble bacon, and set aside. Add onion, bell pepper, 1/4 teaspoon salt, and garlic to drippings in pan; cook 4 minutes or until tender, stirring frequently. Stir in lima beans and corn.
Place flour in a small bowl; gradually add 1/3 cup milk, stirring with a whisk to form a slurry. Add slurry, remaining 1/4 teaspoon salt, remaining 1 cup milk, and black pepper to corn mixture; cook over medium heat 2 1/2 minutes or until thick and bubbly. Remove from heat. Add cheese; stir until cheese melts. Spoon into an 8-inch square baking dish coated with cooking spray. Sprinkle with the cracker crumbs and bacon. Bake at 375° for 20 minutes or until lightly browned on top and bubbly around edges.