Heat the oil in a 12-inch skillet over medium-high heat until shimmering. Add the onions, garlic, chili powder, oregano, tomato paste, cumin, pepper flakes, and a pinch of salt and cook, stirring often, until the onions are softened and lightly browned, 10 to 12 minutes. Stir in the diced tomatoes with their juice, scraping up any browned bits. Transfer to slow cooker.

In a now empty pan, add the ground beef, breaking up into bits. Cook until no longer pink, about 3-5 minutes. Stir in ~1/2 of the tomato puree to scrape up any browned bits. Transfer to slow cooker.

Add the remaining tomato sauce, beans, soy sauce, and sugar into slow cooker. Cover and cook on low for 6-8 hours or on high for 3-5 hours. Taste and adjust seasonings if necessary. Serve with the lime wedges, sour cream or greek yogurt, cheese, jalapenos, green onions, and/or cilantro.