This seems like the most common cause of problems that people are seeing here - there's no way to really stop an enemy from running past your defenses and rendering chokepoints irrelevant. It would seem like this could easily be fixed like so:
Make Phase Jump Inhibitors prevent hostiles from using phase lanes that connect two planets which both have a friendly PJI in them.
This would be good because an attacker would need to destroy the PJI at a planet before being able to progress further into his opponent's territory, so he couldn't just circumvent the map layout entirely, as he can now.
However, apparently PJI locked traffic in beta and created problems. Would those same problems be present if they worked the way I describe here (ie, PJI do not prevent retreat, but must be destroyed to proceed)?