The 6 volt batteries tend to have thicker lead plates in them so they are better at low drains over longer periods. The 12 volt batteries have thinner plates so they can put out more amperage quicker but for less time. One advantage to 12 volt is if one battery dies you can still make due with the single battery for a time. Batteries in series need both batteries to function. I also have had better luck replacing one 12 volt than replacing one 6 volt battery. In series you will only get what the weaker battery has to offer as the currant has to flow through both batteries.
It also depends on what type of loads that you have. I am running an air conditioner off of my solar, so I need batteries that can not only put out surge currant for starting the compressor motor , but also recharge quickly. When clouds go over the solar panels, the batteries have to bear the load. When the sun is back out the solar needs to run the A/C and recharge the batteries. I went with two 12 volt. As long as they can run a fan and my refrigerator over night, My solar will recharge them quickly once the sun comes up, ( I have 960 watts on the roof).
I am happy with my 12 volt Walmart maxx 29DC batteries, But most likely someone will jump in and tell you what an idiot I am because I don't jump on the deep cycle band wagon. For me, deep cycle would not work. Paying $400 per battery also will not work. If my $100 Walmart batteries die in two years, I can go to any Walmart and get a new one for free. If they die after that, oh well I got more than my money's worth out of them.
Figure out what your loads will be and how much time it will take to replace that energy. If you are running a low load for a couple of days before a recharge, (maybe because of weather), a deep cycle may be for you. If you recharge by driving or with a generator and battery charger every day, you may want something that takes a charge quicker so that you can turn off your charger after a couple of hours. The maximum rate that you can charge two six volt batteries in series is what a single battery can take. The maximum rate of charging two batteries in parallel will be double what a single battery can take, (each battery will take half of the currant). If you have a kick ass charger, do you want to spend half the day recharging at the lower rate?
The same size shoe does not fit everybody. What fits one may not fit most. Don't let experts insist what you should use.