I have never been completely satisfied with the arguments for putting 2 batteries in parallel. It seems to me that, unless they are EXACTLY equal and remain so throughout their lifetimes, the weaker one will inevitably drag down the stronger. This would mean that some of the capacity of the stronger goes to helping (i.e., charging) the weaker rather than doing useful work.
If, instead, these unequal batteries were connected in series, then both their output voltages would sum, and this voltage would diminish as the capacity of the weaker approaches its limit. If one battery were weaker, the total voltage might be less than the parallel arrangement, but there would be no capacity "wasted" by the stronger battery trying to charge the weaker.
For the series configuration, I worry a bit about the charging process. I assume that the 2 series batteries are charged together from a 12V charger. If the batteries are unequal in actual capacity, I don't know how the charging current would be distributed or if both batteries in a series configuration would be charged fully and properly. It would be better to separate them and charge each one from a 6V charger, but this is unlikely to be practical. Of course, a somewhat similar concern could be raised about combining 2 batteries in parallel and charging from a single source.
Comments?
-- John H