Season the brisket. Pat the brisket dry with paper towels and season generously with salt and pepper on all sides.
Layer the onions and brisket. Place half of the sliced onions in the bottom of the slow cooker, then set the brisket on top.
Make the sauce. In a bowl, whisk together the beef stock, tomato sauce, red wine, apple cider vinegar, tomato paste, brown sugar, dried onion flakes, Worcestershire sauce, garlic powder, paprika, and red pepper flakes (if using).
Cook the brisket. Pour the sauce over the brisket, then top with the remaining onions. Cover and cook on low for 7-8 hours or high for 5-6 hours, until the brisket is fork-tender.
Skim excess fat. In the last hour of cooking, use a spoon to skim off any excess fat from the sauce.
Slice the brisket. Remove the brisket from the slow cooker and transfer it to a cutting board. Let it rest for a few minutes, then slice against the grain into ½-inch thick slices.
Thicken the sauce. (optional) In a small bowl, mix 1 tablespoon cornstarch with 1-2 tablespoons water until smooth. Stir it into the sauce in the slow cooker and let it cook for a few more minutes until slightly thickened.
Serve. Place the sliced brisket back into the sauce to keep warm, or serve immediately, spooning the sauce and onions over the top. Garnish with chopped parsley.