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What is the difference between a cyclotron-produced and reactor-produced radioisotope? 

The radioisotopes made in cyclotrons complement those made in a reactor.  Atoms with extra neutrons in the nucleus are called neutron-rich and are produced in a nuclear reactor.  Atoms with extra protons in the nucleus are called neutron-deficient and are produced in a particle accelerator such as a cyclotron.  Neutron-rich and neutron-deficient radioisotopes decay by different means and hence have different properties and different uses.  It depends on the radioactive properties required whether a nuclear reactor or a cyclotron is used to produce the radioisotope.  Isotopes produced in a cyclotron typically have shorter half lives than isotopes of the same element that are produced in a reactor.  This is why cyclotrons are located in hospitals, closer to the patients that require them.