Affleck helping Goyer is good to me. I still think Goyer's DC work has a scale beyond Marvel's in terms of character building and conflict creation. His dialogue and a few failures in some scenes are the only things I really see as flaws. He gets villains better than most, while I think Affleck has demonstrated a better understanding of casual human interactions.
I personally feel they should embrace the Sci-Fi aspect from MOS for the new Batman and shared universe, complete with the escalation theme and more realistic world response to them. The Codex idea sounds like a way to begin exploring characters like Parasite (an adaptable organism that copies any genetic material it connects with via the Codex's storage ability), Bizzaro, Superboy, and Match(if the codex is supposed to evolve to allow for propagation of the species, it might be capable of causing various u stable clones to be grown).
And Batman with Sci-Fi technology in an arms race with Luthor sounds infinitely more awesome if their creations have repercussions and counterparts in the DEO and rest of the world. Less "here's the hero's macguffin, never to be matched," or " the alien army has advanced technology yet also is completely vulnerable to old fashioned bullets and bottleneck holding tactics." And let's face it; hard Sci-Fi can work just as well as the softer stuff in the Marvel world, and can provide a wonderful contrast when Hal Jordan doesn't understand a word of what's happening, but Barry does even if he can't quite match it.