Audience-Alienating Premise: The changes New Line made in order to avoid the controversy from the novels included changing the villainous organization, the Magisterium, from a clear parallel of the Catholic Church to a more generic Evil Empire. This ended up pleasing no one: the people who were complaining in the first place were not the sort to back down over a slight story change, and the fans of the series were outraged at such a capitulation and wondered why the studio had bothered getting the rights to such a controversial series if they weren't prepared to go all the way with it. This led to the film becoming a Box Office Bomb.
Germans Love David Hasselhoff: One of the largest cases of this along with the like of WarCraft. Its overseas take was more than four times what it made in the US. Unfortunately, New Line sold the overseas rights cheap.
It didn't help that New Line announced from the start that the criticism of religion would be completely neutered, which ended up pleasing no one. The religious right thought it still wasn't enough, and the fans were left wondering why they would adapt such a controversial book series in the first place if they were so worried about this.
Despite these issues, some admire the developers for arguably having a more loyal grasp of the source material than the film executives. Several incidents from the novel omitted from the film were incorporated almost word-for-word, and the game notably follows the original sequence of events, avoiding the film's subsequent restructuring. To date, playing the game is the only way to view some of the cut footage. Though clunky execution and less-than-stellar graphics mar the overall experience for most gamers, it can be appreciated as a sincere attempt from a story standpoint.
Visual Effects of Awesome: Say what you will about the film, but there's no denying that it has a lot of truly spectacular visuals, particularly the airships. It even won an Oscar for Best Visual Effects, beating out Transformers (which many people expected would get the award).