Preheat the oven to 350 degrees F. Season the brisket with salt and pepper. Heat a large cast iron skillet over high heat and add 2 tablespoons vegetable oil. Sear the brisket until browned on each side, 6-7 minutes. Add beef stock, pomegranate juice, water, onion and cinnamon stick. Cover and braise in the oven until fork tender, 2-2 1/2 hours. Remove from the oven and allow the meat to cool slightly before shredding. Reserve the onions and 1 cup of the braising liquid.
Heat a skillet over medium heat. Add 2 tablespoons vegetable oil and stir in the chili powder and cumin. Cook on medium for 2 minutes. Fold in the brisket and the reserved onions from the braise. Season with salt and pepper. Stir in the braising liquid to deglaze the pan. Cook until heated through.
Cut the top off the pomegranate, score the outside vertically along the veins, then pull sections apart. To remove the seeds, hold a section over a bowl and smack the peel with a wooden spoon to release the seeds. Mix pomegranate seeds (approximately 1 cup) cilantro, red onion, jalapeno, and lime juice in a small bowl.
Add brisket to each tortilla, then top with pomegranate cilantro salsa and cotija cheese.