The answer depends on who you ask.
Either would be a fine choice. Because I have success with and prefer Nvidia chipsets I would go with the 780i and 2 8800GT sli setup.
And I understand that some people hate Nvidia chipsets, everyone is entitled to an opinion. I also understand that X38 is a better overclocker and supposed to be a more stable chipset.
But I like my games and so far I haven't had any problems and enjoy my SLI performance for the price very much.