Lack of actual story is a big one. Lack of any characters to develop a story is even bigger. Getting bits of lore from random documents in this game does not generate a strong story line.
...its a multiplayer survival game, not a story driven RPG... seriously, people act like they actually expected a story from the damn thing. they were very direct in stating that the story would be piecemeal and fed to you by robots and notes.
Besides that, there is a story and a rather interesting one at that. Story spoilers:There are no NPCs because they are all dead. There is a plague that infects not just people but any and all creatures and turns them into a hive mind of killing machines. The plague is spread by mutated bats called scorchbeasts who carry a mutated virus and were created by the mining companies using nukes underground to mine faster with complete disregard for the safety of the workers. So anyway, there are numerous factions that all had to deal with this, the Raiders, Responders, Freestates, Brotherhood of Steel, and the Enclave. I wont go into detail about the factions themselves but as you find out through the main quest, they are all dead. Every one of them has been wiped out by this plague or the other dangers of the wasteland. The Brotherhood has determined that unless stopped, this plague and the scorchbeasts are an extinction level even and could go on to wipe out all live on the entire continent. You also find out that the factions all distrusted each other and refused to work together. They all individually had the pieces required to stop the plague but through paranoia and distrust (or lack of desire in the case of the raiders), none of them succeeded and literally all of them had died. The actual quests of the main quest have you going to each of the factions and gathering the pieces yourself. ---
From the depths, the thing they called Worm King did rise. Nirn itself did scream in the Mages' and Necromancers' war.