It used to be, EPR was more representative of thrust than N1. That was somewhat offset by EPR being more susceptible to error than N1.
With FADEC engine control, EPR became less susceptible to error - the FADEC could compare inlet pressure to aircraft total pressure, and model outlet pressure based on other engine parameters to compare to measured exit pressure. EPR also had other advantages relative to N1 - thrust at N1 is more dependent on ambient conditions (temp and humidity) than EPR. Meanwhile N1 powersetting had to account for the ambient uncertainties.
Short story, N1 had to "give away" thrust to insure takeoff thrust was available.
As newer engines go to ever high bypass ratios (already approaching 10 to 1), combined with the inherent difficulties in measuring EPR, I expect N1 to become the predominant power setting parameter in the future.