Solar: Reason For Joining Batteries/Solar Panels in Series
It's a tradeoff between voltage and current.  If you put the batteries in parallel, then you have a higher current, but lower voltage.  In this case, you need thicker cables to connect to the batteries, or put up with more power loss - the power lost is proportional to the SQUARE of the current.

Also, the semiconductor devices in the charging circuit will typically have a fixed voltage drop across them when they are conducting.  Therefore, if you can reduce the current, you reduce the power lost, and improve efficiency.  Higher-voltage semiconductors will have a higher voltage drop, but not enough to counteract the savings from the reduction in current.

Furthermore, there are other advantages depending on what is being driven.  Remember that the battery voltage is going to fluctuate depending on the charge state of the batteries.  If you need a steady, regulated 12V output, then it is much easier to provide this from a 24V-ish supply than a 12V-ish supply - stepping down DC voltage is easier (and therefore more efficient) than stepping up.  As the batteries get into a lower discharge state, the output regulation will find it easier with the 24V-nominal supply.