The (Roman) Empire
After the Septim dynasty is gone, the Empire's power started waning.
This can be compared to the Romans, who's waning power was the cause of the real life Dark Ages.
It can also explain the lack of central guilds in Skyrim. The Fighters and Mages guilds are empire sponsored. In the state the Empire is now in, sponsoring such guilds in Skyrim, which verges on seceding, would be very difficult.
The Aldmeri Dominion/The East Roman Empire
This is not the best comparison, but there are some similarities. Both were once part of the The Empire and breaking away is what some believe was the first step towards the Dark Ages.
The Dominion weakened the Empire by attacking it, forcing the Empire to put its resources into defending what is left. The split between the Roman Empires caused a serious lack of resources for the west Roman Empire. This caused the west Roman Empire to not being able to defend itself against the 'barbarians'.
The barbarian hordes and the Stormcloaks
Because the Romans were losing power during the start of the Dark ages, barbarian hordes started to regain control of their territories. Stormcloaks are doing the same. They use the Empire's weakened state to go back to the true Nord ways. This also caused an 'every hold/village for himself' mentality
Religious Conflict
This also played a role in real life when the old pagan religions became outlawed. And in Skyrim, where Talos became outlawed. This causes a huge conflict between multiple groups. I will not go into further details, to avoid toughing sensitive subjects.
Racism
When the Roman Empire was the main power in Europe, travelers were much more common. Therefore people of other races were a bit more accepted. When the Dark ages began, infrastructure was pretty much broken. Everyone who left the village had no insurance of returning and people did not know what happened outside. Therefore everything that was different was treated as evil.
I do not know how Skyrim was during the Empire's prime, but if the Empire is in charge, it would have been much less pro-Nord than it is now.
Dragons and the Black plague
Both were considered supernatural. Both are very destructive and the people are powerless to fight against them.
So, that was all I can think of. I do hope its not complete and utter nonsense. Like the things M'aiq would say.
Please tell me what you think.