A few weeks ago a fan theory came to light about Destiny's story, which essential posited that actually, the Traveler and the Speaker weren't quite as benevolent as they appear and may actually have been the Darkness rather than the Light.
According to a Bungie game tester, who is breaking his or her NDA to reveal this information, it seems that the theory may actually have some truth to it after all.
“The story revolved around discovering that there was something wrong with the Speaker and the Traveler. As a Guardian, you were abducted by this yet to be named group led by Crow (a deleted character)…The Traveler was the cause of the collapse of the Golden Age because this group found through their travels that the Darkness was a spawn of the Traveler rather than its rival. Essentially when the Traveler was brought to Earth it unleashed the Darkness and took over the technology humanity used and turned it against them. As that happened centuries ago, the truth was twisted through the Speaker to say that the Traveler protected Earth in its darkest moment than destroying it.”
It's noted that numerous locations in the game are named, but are inaccessible. These areas, such as King's Watch, could be reached through a glitch in the beta but appear to be completely removed from the main game and suggest lots of locations, such as Old Chicago, were cut.
As for Crow, some believe he is in fact the Reef Queen's brother, who made it into the game with a much diminished role. As the changes to the story appear to have happened within the last year, many have suggested that they have something to do with the departure of writer Joseph Staten in September 2013.
To fill in for the gaps in the story, someone was hired late in the game's development to write the grimoire cards, this is also why the lore doesn't appear in-game, as there was no way to implement a lore codex at such a late stage.
It seems highly unlikely that Bungie will comment on cuts to the game's story and it's possible much of what was left out could be re-introduced later through DLC but if large sections of the plot were removed it would explain a lot about Destiny's poor narrative.