There are many factors that go into what value compensation should be set at. There are three big ones.
Expertise, in particular, plays a large part because an experienced model arrives on time (and sober), knows how to interact with the camera and the photographer with minimal direction, assumes appropriate poses naturally that fit the context of the scene, pauses at the right times as to minimize the number of discards, and she can make facial expressions look genuine. The higher compensation comes from making the photographer's job easier and producing higher quality product in a shorter timeframe.
The model's looks also play into the equation, primarily because that sets the demand for the model and in turn that affects availability. Basic economic models of supply and demand clearly state the higher the demand, the more things cost. Hence a model that isn't in as much demand will likely be unable to command rates that one is. This is why models should to TFP deals to build their portfolios in order to raise their demand, even if just from gaining additional experience.
And the other primary factor which affects cost is how much skin the model is willing to reveal and what she's willing to do in front of the camera. Unlike looks, this is one area where all models have total control. It can also be one of the bigger money makers.
The photographer has to determine a rate that factors these accordingly, and many other things (availability, short-term notice, ...) as well into the compensation rate.
Just because two models are willing to stand in front of the camera for equal time does not mean they are providing equal value to the photographer. [It is also true that multiple photographers do not provide equal representation value to a model, which is why one looks at a photographer's portfolio before accepting a trade-based assignment. Skill, equipment, and post-processing abilities are the parameters the photographer has to measure up to.]
Here's a reasonable compensation paradigm that is actually fair to both parties equally: