In a large stockpot, melt 2 tablespoons of olive oil and 2 tablespoons of butter over medium heat.
Add the pretzel cubes and cook, stirring frequently until golden and crunchy. *Note - watch the croutons closely as they burn quickly.
Remove the browned croutons and set aside.
Add the prepared bratwurst to the pan and increase the heat to medium/high. Brown the sausage, stirring occasionally until browned well on all sides.
Remove the sausage from the pan and set aside.
Add the remaining olive oil and butter to the stockpot along with the chopped onions.
Stir well and add the salt and pepper.
Continue cooking and stirring the onions occasionally until the onions are golden in color and reduced in volume (approximately 12-15 minutes).
Add the flour to the caramelized onion and cook, stirring well for 1-2 minutes.
Slowly add the beer and beef stock to the pot.
Stir in the brown sugar, bay leaves, and grated nutmeg.
Reduce the heat to medium-low and add the browned bratwurst back to the pot.
Stir well and simmer for at least 15 minutes, longer if you have the time.
Remove the bay leaves.
Serve the German Onion Soup topped with the pretzel croutons and the shredded Swiss cheese.