I have done both before, although I guess you meant that the 12 volt batteries were hooked up in parallel as two 12 volt in series would give you 24 volts.
I found a few things having used both 12 volt and 6 volt batteries over the years. One important thing is to look at the amp storage for the batteries.
One 6 volt battery I saw in an RV only had 75 amps of storage. That is almost useless unless the RV will always be hooked up to shore power.
Another item is one of those that Roy pointed out; the amp-hour storage of two six volt batteries in series (to make 12 volts) is only what the amp-hour rating of a single battery is. As an example, each of my 6 volt batteries hold 275 amp-hours of storage. Hooked up in series they still only have 275 amps of storage.
Next is my opinion. I have used Trojan brand 6-volt batteries for many years. I boondock and charge off solar panels almost exclusively. They are superior quality, charge fast and seem to hold a charge well. The last set I owned lasted 11 years, and I used them in two trailers. When they started showing signs of aging I still used them another 2 years. I now use four of them and they are great.