Having done both, I now favor the series 6V battery solution.
As Dan pointed out, you have more capacity and a more serious deep cycle setup, for a theoretically longer life, at a more reasonable price. The 6 volt batteries are somewhat taller (1.5 to 2 inches taller for similar length and width).
The point about having a second battery in case one goes bad in the 12V situation is generally false. Unless you use the two batteries independently and separately, if one 12V battery goes down while in parallel, it's going to take the other to at least a deep discharge before you even know you have a problem. Don't ask me how I know this - but I'll tell you anyway.
I don't know exactly what happened. I found both 12V size 24 marine/deep cycle (1.5 years old) down around 11.5 volts, and not charging with the A-frame plugged in. Found the 30 amp fuse (connection to battery) blown on the Wifco converter. Hooked up a Sears 10 amp charger to the battery bank after disconnecting the bank from the trailer. The charger kept popping its circuit breaker, so I separated the batteries. Recharged one, but still had a popping circuit breaker on the second.
Next was a very stupid SPUT (Stupid Pop UP Trick). I put the batteries back in parallel, thinking the charged battery would help the charger charge the low battery. Wrong! The #6 paralleling wires glowed red hot, melted their insulation, and flamed from the hydrogen discharging from the battery vents of the low battery. There were also small flames from the cell vents. I retreived a set of electricians pliers and with my hands completely on the insulated portion of the handles, cut the paralleling wires. The flames died out immediately.
When I cleared the debris away later, I had holes in the tops of both battery casings. After some researching as to what would fit my battery box, I found 6V 232AH golf cart batteries at Costco at $150 for the pair. I bought/made up new cables, and installed the marine 2 battery selector switch I had bought months ago for a shut-off (not standard on PUPs and A-frames).
The new arrangement gives me 116 usuable amp hours instead of 80, and much less of a potential fire hazard if something goes wrong. And the price was less than two 12volt replacements.
Fred W - I hate learning from my own mistakes, would much prefer to learn from others'.
2014 Rockwood A122 A-frame
2008 Hyundai Entourage minivan
PS: My converter fan now comes on when recharging if the batteries have been used for a couple of days of dry camping, showing a higher charge rate. Life is good.