When we say which one has higher potential energy. In context of typical physics textbook, comparing the potential energy of two points does not take the path into account, since the final potential energy is independent to the path. However, in orbital mechanics, the path becomes important because the energy spent on the path translate into the among fuel required of the SV (space vehicle). That is what the interplanetary transport network is all about to save fuel of the SVs. To take the least among of fuel to take an SV from A to B is the goal here.

However, this network is not very useful for manned interplanetary travel, since it is too slow. There are other orbit maneuvers, like powered slingshot that can reduce the time.