Heat a dry heavy skillet over medium-high heat. Char the cut sides of onion and ginger for 6 to 8 minutes until dark patches form; add star anise, cinnamon, cloves and coriander for the final 1 minute, stirring the spices.
Transfer the aromatics and spices to a large pot with broth, water and chicken thighs. Simmer gently for 30 to 35 minutes until the chicken reaches 165°F.
Remove the chicken and strain the broth through a fine sieve, discarding the aromatics. Return the broth to the pot and stir in fish sauce and sugar.
Cook rice noodles in a separate pot according to the package, then drain and rinse briefly with warm water. Pull the chicken from the bones and shred, discarding the bones.
Add bean sprouts to the simmering broth for 1 minute. Stir in lime juice, then divide noodles and chicken among six bowls.
Ladle the hot broth and sprouts over the noodles and divide the sliced scallions evenly among the bowls.