I don't know if I can choose between Shaun of the Dead and The World's End. Initially, I would have said Shaun. However, I've seen World's End around 4 times now and it gets better every time I've watched it. Unlike Shaun and Fuzz, I found The World's End takes a few viewngs to start appreciating it. There are some really terrific scenes.
The challenge that Wright/Pegg had with World's End was balancing the amount of screen time the main characters had. In previous films, they wrote the films so that Pegg and Frost were to have the majority of the screen time and character development. However, with World's End, they challenged themselves by adding in the group dynamic, which was a whole new challenge. Having to spend time with three more actors and adding in Rosamind Pike as the love interest meant less screen time for the duo. This is why it takes further viewings to appreciate it. I found that I had to take a different approach in watching it than I do when going into Hot Fuzz and Shaun of the Dead.