Okay, I know that there is a lot of people that want Phase Jump Inhibitors to completely block phase jumping, and there is an equal amount that disagree.
So, here is an idea... more of a compromise.

Phase Jump Inhibitors could block jumping to colonized territories. This would require two PJIs. The PJI would act as a sort of gate on the Phase lane to prevent enemies from using it. This also requires that the player possess both locations.
This would prevent ships from rushing passed planets, and it would allow the player to establish better defensive locations. It'd also be a nice way to prevent enemy scouts from seeing you full territory. It's always unfortunate when the enemy gets to take a look at your whole fleet and defenses with so little effort.