I have both, and don't find much difference. I'm left-handed, but I don't think it's really relevant. One consideration might be whether or not you ever intend to use the bag with a bivy sack...you might want the zippers on the same side, assuming the bivy had a zipper. Or maybe opposite sides...I don't know.

Having thus muddied the waters, let me add another variable. I have a mating pair of old Trailwise Slimline bags, and the draft flap on one is attached to the bottom side of the bag, and to the top on the other. That way the zipper on the bottom is covered when they're mated. Not all manufacturers do this, maybe not any these days, for all I know. It's something to check for, though. Having the draft flap attached to the top of the bag insures that it will hang down over the zipper, rather than possibly falling away from the zipper. A thick, well designed draft flap minimizes this possibility, though.