Preheat oven to 425°F (220°C). Spray a baking dish with nonstick spray.
In a small bowl, combine 1 teaspoon smoked paprika, 1/2 teaspoon salt, 1/2 teaspoon pepper, 1/2 teaspoon cumin, 1/2 teaspoon chili powder, and 1/4 teaspoon garlic powder. Add 2 tablespoons olive oil and stir to form a paste.
Pat the 2 pounds boneless, skinless chicken thighs dry with paper towels. Rub the spice paste evenly over all sides of the chicken thighs.
Spread the sliced sweet onion across the bottom of the prepared baking dish. Arrange the seasoned chicken thighs on top of the onion. Tuck lime wedges (from the 2 limes) between and around the chicken pieces.
Cover the dish tightly with foil and bake 45–60 minutes, until the chicken reaches an internal temperature of 165°F (74°C) at the thickest part. Remove from oven, discard foil, and transfer chicken to a cutting board; let rest 5–10 minutes.
While the chicken rests (or a few minutes before you plan to shred it), make the goat cheese queso: heat a small saucepan over medium heat and add 1 tablespoon unsalted butter.
When the butter is melted and sizzling, add 1/2 jalapeño pepper (diced) and 1 garlic clove (minced). Cook 1–2 minutes, until softened and fragrant.
Whisk in 1 tablespoon flour and cook 1–2 minutes, whisking, until the mixture is golden and bubbly.
Gradually whisk in 1/2 cup milk, reduce heat to low, and cook, whisking occasionally, until the mixture is slightly thickened.
Add 6 ounces crumbled goat cheese and stir until completely melted and smooth. Taste and season with salt and pepper if desired. Keep warm over low heat, stirring occasionally.
Shred the rested chicken with two forks or chop it, as you prefer.
Warm corn or flour tortillas according to your preferred method.
Assemble tacos: place shredded chicken on warmed tortillas, spoon over the goat cheese queso, then top with chopped tomatoes, sliced avocado, sliced red onion, and extra crumbled goat cheese. Serve with lime wedges.