The other big advantage to using a pair of 6 volt batteries are the way they are connected to get 12 volts. If you trace the current path through a pair of series connected 6 volt batteries, there is one and only one way for electricity to flow through them. This means all of the cells get equal amounts of charging current, and all contribute equally to the load when you're using power.
With a pair of 12 volt batteries connected in parallel, there are two paths the current can take - part of the current flows through one battery, part flows through the other. This means unless the batteries are precisely matched, one will draw more charging current than the other. Likewise, when you use power, one battery will contribute more power than the other. This makes it harder to get full capacity out of both batteries.