At the Wondercon panel with Scott Snyder, CBR quoted him on his plans for Zero Year, saying that "With 'Zero Year' we're absolutely, 100% [doing new takes on old ideas]." He continues to explain that he will be writing an entirely new story, different from Year One. It will, of course, include essential aspects such as "the pearls in the alley," but otherwise it will be "a Gotham you've never seen before!"
Personally, I'll be happy as long as the ending ties up all the loose ends (as in, no villains escaping into the unknown, and no mystery or puzzle left unsolved).
Edit: I summarized Snyder's plans incorrectly. They are fixed now.