Slice bacon into 1/4" strips and brown over medium heat in an 8" skillet until crispy. Remove from the pan and set aside. Add chopped onion to the pan and saute until it starts to get soft, about 5 minutes then add the garlic and continue to cook for another minute. Don't let it burn. Add the Lima beans and just barely cover with water, cover and simmer for about 15 minutes until the water has evaporated. Give the beans a taste and if they still have a waxy texture to them add a bit more water and continue to simmer for a few more minutes. When the Lima beans are soft add the corn and red pepper flakes, (if desired) along with the cooked bacon and heat to serving temperature. Season with salt and pepper to taste and serve.
Wait to add the salt until the very end of the cooking process. Salt has a tendency to break down the beans and if you add it during the cooking process you may end up with a big pot of mush, and that is not what you want.