Bill,
It's strictly a matter of physical space and the number of Am-hours you want available. The GC2 and GC2H 6v "golf car" batteries are a different shape than the typical 12v deep cycle, which will typically be BCI case size 24, 27 or 31. The 12v are usually longer and lower than the 6v GC family of sizes.
As kdbgoat says, the main advantage is that you can get a pair of true deep cycle 6v GC batteries for much less costs than true deep cycle 12v's with similar AH capacity. Often 40% less (prices vary by locale). Gold Car batteries are produced by all the major battery companies and in high volumes, so the pricing is better than 12v deep cycles, which is a niche market .
You can look at the case sizes online - find a BCI battery size chart. GC2 and GC2H (higher) batteries typically provide 210-230 AH per pair. A pair of Group 27 size 12v deep cycles would be about 210 Ah and a pair of Group 31 size 12v's about 230 AH.