The problem is the depending on the circuit you cannot always put a phototransistor in place of an LDR where the circuit needs a resistance, not a voltage source. An example would be putting an LDR in the feedback of an opamp where the gain would change with light level. You could not easily substitute a phototransistor in that sort of circuit. Similarly you could put an LDR in place of one of the timing resistors in a 555 but not a phototransistor. It is easy to imply step or sweep a resistor value so I would have though that would have been the easy solution in most cases.
Keith.