Drizzle a large pot or dutch oven with olive oil. Brown the sausages lightly on both sides over medium-high heat. (This step is to infuse the onions with flavor. If time doesn't allow, skip this step.) Remove sausages from the pot.
Add the onion to the pan, stir just to deglaze the bottom of the pot.
Next add beer, garlic, salt, black pepper, crushed red pepper flakes and thyme. Bring to a rolling boil. Add the sausages back to the pot. Immediately lower the heat and simmer covered for 10-15 minutes.
Grill: Meanwhile, heat a gas grill to medium-high. Oil the grates. (Alternatively, you can use a grill pan on the stovetop.)
Uncover and remove bratwurst from beer using tongs allowing excess sauce to drip off.
Cook bratwurst on the preheated grill over medium heat, turning occasionally until no longer pink in the middle, 8-10 minutes. An instant-read thermometer inserted into the center should read at least 160°F (70°C).
While grilling brats, simmer the onions uncovered on the stovetop until the liquid has reduced and the onions are a deep brown color and caramelized, stirring occasionally. (Tip: You can add a tablespoon of butter to the onions for extra richness.)
Serve beer brats immediately topped with onions on warm buns and mustard.