When you travel between harbours in SS2008 you will enter an open sea scenario before you reach you destination. I think it works just fine. For instance, a typical voyage across the North Sea between Esbjerg (DEN) to Harwich (GBR) will take 17 hours! Do you really want to spend that many hours on one single mission?? The interesting parts of that voyage is leaving port, maybe some heavy traffic in a separation scheme and finally the approach. This is exactly how it works in SS2008.
I agree that the interesting part is to enter and leave a harbour, but it could be done like this: Make a waypoint you can jump to when you prefer". I think the jump is done too soon, as I would like to sail out of the harbour and experience the change in the waves as you enter open sea, or coming from open sea and see the land appear in the distance and getting larger and larger. If you want to skip that, hit the jump button, if not just sail away.
Another way is to increase time count. Time count should slow down to 1 when something interesting happens. It is just like that in Silent Hunter.
It is also strange that after a jump has been made you are then dead still in the water.