batteries connection series-parallel vs parallel-series
Is there any difference regarding end voltage/capacity ?


Theoretically, if all cells are identical, no. In the first case you first add the voltage and then double the capacity (assuming the cells are identical). In the second one you double capacity and then add the voltage.

However cells are always a little bit different. If you start using cells in series with different initial states of charge, there is a risk that a cell goes empty before the others (and one may become critically empty whereas the others are ok). And you will not be able to see it.

It is generally not a problem for some technologies like NiMH, however for lithium-based cells an overdischarge is highly dangerous. That's why a Battery Management System (BMS) of a lithium cell battery will monitor each voltage to balance them safely.


  If not, what's preferable ?


In the case of lithium battery, the second one is preferable. Because the pairs of parallel cells will be automatically balanced and at the same voltage. So you only need to watch the 2 pairs of cells. However in the first case you will have to watch the four cells individually.

Hope it helps.

Best regards,