Good point, but the atmosphere of CO/CO2/N2, which is what is thought it was now is just as suitable as CH4 and NH3. [
1] . The key is the lack of O2, which should not have come up until photosynthetic organisms did.
Also check out the Murchison meteorite. Assuming these were common in the early solar system, amino acids could have very well have come from space. Theoretically a molecular cloud could create the building blocks of life, but these theories are all as recent as 2004.
Also, this is not to say Mr. Miller was a genius and solved everything in a simple experiment. His experiments have been redone countless times with different atmospheres. Also, there are indications that there may have been a significantly higher amount of H in the atmosphere, which would have seriously hindered any natural creation.