Quick comment: because you already have the D3S not the D3 I would stand pat. Much as I love my D4,it seems logical the 3S is the better shooting companion to a 3X. And you'd have to stretch to see a resolution difference between 12 and 16mp I think.
I'd consider waiting a generation to see what the D4X and D4S bring to the table. If you shot video I'd get a D4 and tolerate the battery difference.