Well who would have thunk it? According to a massive report from Kotaku's always informative Jason Schreier, Destiny as we know it was cobbled together in a very short space of time following the decision to scrap its original story.
Sources say that upon showing Bungie's top brass a 'supercut' of the title's major plot points, the senior staff members weren't impressed - and this was in 2013, a year before the game would eventually release. Basically, this means that the writing team had less than 12 months to create an entirely new narrative that could still work alongside some of the missions that the developer had already crafted. No wonder it lacked any kind of cohesive structure.
Apparently, the original plot had a lot more to do with the artificial intelligence known as Rasputin. It also featured more characters, and each mission was to be bookended by cutscenes, some of which were supposedly lengthy cinematic scenarios. One interviewee even states that the Dreadnaught - the new location from The Taken King expansion - was originally going to appear in the main release, and that it'd play host to the last third of the plot. When the story was slashed to bits, the Dreadnaught was cut completely and moved to one side, ready to be reused at a later date.
Likewise, the plot itself was shoved away from the spotlight as the studio ramped up for the shooter's release. Instead of spending any more time on its now butchered narrative, Bungie focussed on polishing existing gameplay mechanics, and so we were left with a half-baked story that had been stitched together as quickly as possible.
Certainly answers a lot of questions, doesn't it?