I also thought: "Hey we should have something like this in Battle Stations where players can defend and assault a control point. It's like the clan wars but it's PvE and you can do it frequently instead of waiting for the clan fort to rez."
So basically we can set up control points between certain ports. The Imperial City is at war with Al Amraan so it's not unexpected that there'll be a blockade of sorts. If you travel between these cities while the blockade is up you'll encounter NPCs which will attack you. If you survive you can still get past the blockade.
There'll be a fixed number of NPC ships in the blockade (maybe a mobile fortress as well) and if players manage to sink all the NPCs the blockade will be removed (for a while) and players can travel between the cities freely once again.
Why we trashed the old ship system
There are gameplay reasons (trying to remove the huge power difference at level multiples of 5 and 10). Another reason we got rid of the old ship system because this is how we want to render our ships from now on:
... and we can't make 50+ of these ship designs which is why we have the new ship system to make all ships last longer. I've yet to assign this design to a particular ship (yes this what it'll look like in the game).