Need help with an NES controller code

Are you sure you want to execute the second loop 15 times? o.0

I'd have guessed you wanted this instead:

  // Clock Cycles 2-16
  for (int i = 1; i <= 15; i++)
  {
    digitalWrite(clock1,HIGH);
    delayMicroseconds(4);
    digitalWrite(clock1,LOW);
    delayMicroseconds(4);
    controllerData1[i] = digitalRead(data1);
  }

  for (int i = 1; i <= 15; i++)
  {
    digitalWrite(clock2,HIGH);
    delayMicroseconds(4);
    digitalWrite(clock2,LOW);
    delayMicroseconds(4);
    controllerData2[i] = digitalRead(data2);
  }
}