Insubstantial is half-damage from physical attacks, phasing is going through walls and such. Most creatures that have one also have the other from what I have seen. Wraiths have both, for example.
I think they broke it out into two things to be able to cover different types of creatures. For example, some creatures can phase through walls but when attacking they revert to solid form thus they don't gain the half damage benefit of insubstantial.
And if you think about liquid creatures, they would likely get insubstantial without phasing since being liquid does not allow you to move through walls.