Why Bhutan remained politically not unified till 16th century

1.Visit of religious missionaries:

From the 9th century onwards, many enlightened religious personages played varied roles in the lives of the Bhutanese people and the growth of their distinctive national identity. 

2. Busy propagating Buddhism than political unification:

Hinayana and Mahayana Buddhism practitioners were sent as a missionary in the Himalayan region; They were more focused on the spread of Buddhism in the region than a political overview.

3. Clashes between different sects of Buddhism.