Confusing question. No-one connects batteries in parallel and keeps the capacity the same and I have no idea what "3 or series arrangement" might mean.
How you connect cells depends of what you want to drive. If you need 15V it would be daft to connect 4 cells in parallel and then add a step up converter when 4 in series would do it without any additional circuitry (which is bound to waste some power because nothing is 100% efficient).
But the main point is that whether you use series or parallel connection the amount of energy in a given number of cells is always the same. So the efficiency of any additional circuitry needed makes the difference.
Steve