I think Zack is at fault too, but it seems mostly that Goyer missed the mark on this one.
First of all, we're all talking hypothetically as we haven't seen the movie.
Christopher Nolan has directed
Batman begins on a script by David S. Goyer, and that worked out pretty well! Granted, he rewrote it, yet if you read Goyer's draft it's pretty similar to the end result. Nolan changed some of the dialogue, switched some scenes and flashbacks around; in the end, he made the Goyer's script work better on screen.
It's a director's job to look at a script and to make it a successful movie. Now, Goyer's work here is probably at fault, but the man in charge, and who ultimately is calling the shots and determine how everything works out on screen is Zack Snyder.
A script is just a blueprint. A director can shorten scenes, switch them around, add dialogue, remove dialogue, just as he sees fit. A keen eye for storytelling and characters will do miracles. Editing can, aswell. Every decision a director makes influences the transition from paper to screen. People, especially nerds on the Internet, tend to oversimplify things: it's not just "hey, this is the script, now take a camera and film it. Done." That's not how filmmaking works.

Even a solid script can get bogged down in the filmmaking process. And no, it doesn't need heavy studio interference and constant drama during production for that to happen. Simple miscalculations by the director and/or a faulty approach to the material will do that.