The Stokes shift described the observation that the light emitted from chlorophyll molecules is redder than the light absorbed. This is because higher energy (blue) photons cannot have their excitation energy transferred to the reaction centre, and must instead fall to the S1 excited state (from the S2) by internal conversion. This shifts the chlorophyll emission spectra, when energy is lost from the S1 to S0 excited state as fluorescence, as this will be redder.
However, not all excitation energy at the S1 level is lost as fluorescence - Förster resonance energy transfer (FRET) allows the transfer of excitation to the reaction centre of the photosystem, increasing the turnover and thus the rate.