6-volt vs 12-volt is not the issue per se. It's the quality
of the battery that is the biggest difference.
6-volts have been generally golf cart or industrial machine batteries, which were designed to be more heavy duty (e.g., thicker plates) and be drawn-down repeatedly.
Most 12-volts that are readily available are essentially 12-volt starting batteries or dual purpose Marine batteries. However, the industrial 12-volts rival any 6-volt battery's construction (e.g., thicker plates) but then the weight, cost and size of the battery can be an issue.
So, two 6-volt batteries in series vs. two 12-volt batteries in parallel can provide the same capacity, but the 6-volt batteries will generally last longer when drawn down repeatedly over time (hence the name "deep-cycle").
There is a caveat. As I indicated above, there are quality deep-cycle 12-volt batteries (not marine though) that will be the same quality as 6-volts. Those "true deep-cycle" 12 volts (for lack of a better phrase) can be just as good.
This site is a great resource ... Deep Cycle Battery FAQ
My advise is to step back and look at your needs first:
Do you dry camp a lot (off the grid)?
How much capacity do you need before recharging?