bahun chhetri are also indigenous of nepal (if u consider karnali region as nepal).
and newars though being janajati have been in centre of power for ages.there were powerful kajis,merchants, pradhans, officers, royal priests and jyotish etc.
no ethnic group is/was the ruling group in nepal. it was a small group of thakuri/khas and newar families who enjoyed the state power and not the whole race.