Another advantage I see as converting two "small" ponds into one is evaporation. My first small pond loses an inch over two days in the hot summer months. If I do not get a few good rain shower, I can easily be down a few feet by summer's end. I would guess that a larger pond would not have this problem.
I don't think you would have much difference in evaporation, but you would have slightly more water. Although I would like having two ponds and will be building a smaller one in the near future, for CC.