Missions are there for temporary small boosts if you need them I think. They are not there to guide you or anything even if their bonus is mostly pointless after completing those missions. Missions do guide the AI on the historical path sometimes. For example it allows Ottomans to conquer Levant, or Mughals to expand on other Indian kingdoms, etc.
It also allows for the glorious rebirth of the Purple Phoenix and gives a great reward/guidance system.