Biggest advantage to a pair of 6v batteries for a 12V system vs single 12V is the plate size in the 6V. It will stand up to more charge/discharge cycles as well as supply high currents with less plate damage.
If you have the room, ability to carry the extra weight, and a durable wallet, get the biggest 6V batteries you can.
That said, eventually all Lead/acid batteries will be kicked to the curb as the new battery technology takes over.
I drive a Chevy Volt with a 17 Kwh battery that weighs only 400#.
Can be charged with a 240v charge station in only 4 hours 5,000 charge discharge cycles versus maybe 500 for Lead Acid and only if you only use half the battery's capacity.
17 Kwh from the 400 pound battery versus 1.2 Kwh from a 100# battery. Put four of them together in any configuration you want and 400# of lead acid batteries will only provide a fraction of the capacity the Li-Ion battery pack in a Chevy Volt.
Obviously, the Volt battery pack uses higher voltage (360) but it's an example of what the future holds. Higher capacities, longer service life, less weight.
Maybe the alternative will be here before I have to replace my two 12v batteries connected to a selector switch.