I like how roads work generally but i have two problems with the system.

1. When i build a new settlement i don't believe it has really been connected to my empire if the road that connects it runs through enemy territory. particularly if there is a route that can be built which does not involve going through enemy territory.

2. When  i am at war with someone it is very annoying when you click to attack a city but the enemy you are fighting has a ZOC in the way, at this point the auto route sends you right round  to avoid the ZOC even through you are at war with the person who has the ZOC in the way.