I can answer some of them:
Siege - In sieges the defenders can still retreat and in many cases there is a bug in which they just stop nearby the wall doing nothing until they are killed by the enemy. They only fight to death when in the center of the city because of the bonus.
Navigation restrictions - You can only navigate around the coasts, it is actually historical and prevents both the player and the AI.
Breaching walls - You will get a notification of the wall breached when you click your army and if you go to battle, you will see a breach in the city wall from where you can send your troops to attack.