To make the pickled onions, bring 2 cups of water to a boil over high heat in a medium saucepan.
Add sugar, salt, rice vinegar, garlic, peppercorns and red pepper flakes for the pickled red onions to a container larger enough to hold 2 cups. Stir to combine. Set aside.
Add sliced red onion to a fine mesh sieve. Slowly pour boiling water over the onions and drain. Add onions to the container with the pickling liquid. Cover and refrigerate for 1 hour (the longer the better) until ready to serve.
To make the jalapeño lime aioli, add all ingredients to the bowl of a food processor. Puree until combined. Season with salt and pepper to taste. Set aside in the refrigerator until ready to serve.
To make the hot dogs, heat a large skillet or grill pan over medium-high heat. Partially cook the bacon until the edges are crisp, approximately 5 minutes. Remove from skillet to a clean plate.
Add bratwursts to the same skillet and cook until brown, approximately 2-3 minutes per side. Remove from skillet. Wrap partially cooked bacon slices around the bratwursts, overlapping them as you wrap. You will use about 2 to 3 bacon strips for each bratwurst. Use toothpicks to secure bacon slices on each end of the bratwurst.
Return bacon wrapped bratwursts to the same skillet, cooking over medium heat, turning often. Cook until the bacon is crisp and browned, approximately 5 minutes.
To serve, add bacon-wrapped bratwursts to hot dog buns. Garnish as desired with pickled red onions, cherry tomatoes, sliced jalapeños, jalapeño lime aioli, cojita cheese, crushed tortilla chips and cilantro.