1. Marc Webb Has More Creative Control
With the first film it was clear that Webb would never have that much power in the director's chair. He had only made one film before (500 Days of Summer) that so the studio wouldn't put that much faith into him. This is evident by the much longer backstory of Peter already containing something in his DNA. This explains why his body reacts the way it does when bitten by the spider. Sony decided to drop this part of the film despite the original trailers suggesting it when saying something about an untold story. Apparently they want to stretch the backstory out over several films but I doubt it was Webb who chose to do it that way. There were rumours that he may be replaced for the new one but by allowing him to do the sequel it shows confidence and patience in him by allowing him to build the Spider-Man world the way he wants to. Its also important for franchises to have the same director work on them to keep the same tone and a director who knows the characters can do better things with them, the key example being Christopher Nolan with the Batman Trilogy.