No, I think Snyder and Terrio did pretty well on the story and themes front. Thematically, it tackles the issue of what kind of world would need superheroes and what are the consequences of superheroes. Yea, it's been tackled by Marvel. However, Age of Ultron was far too light in tone for tackling the issue. I have higher hopes for Captain America. In terms of tone, Snyder nailed the depressing atmosphere of collateral damage caused by a vigilante and super powered messianic alien. I also liked that the ultimate resolution for the fight between Batman vs Superman was Batman seeing superman's humanity when Clark's mother was threatened.
There was a lot of unneeded scenes. Sometimes the action was too gratitutious that it truly did feel depressing. However, the core arcs for Superman and Batman make logical sense. I also think Luthor made a lot more sense than most when you read into what he says. Some of what he says hints that he was abused by his father( I think he directly states it when talking to Lois) , and he hates that no hero came to save him from his fathers fist. That's why he wanted the Bat gone, Supes gone, and was tracking metas. No one came to save him so he hates them all.