Fill a large bowl with ice and water; set aside. Bring a medium pot of water to a boil. Add fava beans; blanch 30 seconds. Remove from water; place in ice bath until cool. Peel outer skin from beans; set aside.
Place 4 cups water in a large bowl; add lemon juice; set aside. Remove tough outer leaves from artichokes; cut 1 inch from tip of each artichoke. Trim and peel stem of each; rub all over with lemon half. Place in reserved lemon water.
Heat olive oil in a saucepan over medium heat. Add shallot, garlic, salt, black pepper, and red-pepper flakes; cook, stirring frequently, until shallot is lightly browned, about 2 minutes. Add artichokes, 1 cup lemon water, thyme, and parsley; bring to a simmer. Reduce heat to medium low, and cover; simmer until artichokes are tender, about 14 minutes.
Add fava beans. Cook until beans are tender, about 3 minutes more. Serve hot.