The eye of mangus was a much bigger threat since it could destroy the world. Alduin and his dragon army are just town destroyers, its gonna take him and his dragons months or even years to destroy every living being in every town and city on Tamriel.

The length of time it takes doesn't make them any less deadly or dangerous.

Huh? Of course the length of time it takes makes them less dangerous.

The more time they take, the more time you have to react to it and plan for a solution to stop them. Our sun will expand into a red giant and engulf the earth in 5 billion years, most likely killing everyone. I wouldn't call that more dangerous than nuclear holocaust because we have time to react to it.

Alduin didn't really get started yet. Mundus would have eventually been destroyed.

Until it comes back, that is.

Who said the main quest had to be the most dangerous thing in the game.

Plus lets put it into perspective.
College of Winterhold threat is a Thalmor with a stick and no knowledge of what he is doing.
- Anybody can kill him, just so happens you have to.
- There are better mages than him.
- You really dont have to kill him anytime soon.

Main Quest threat is a legendary Dragon known to bring the end of the world has just appeared and started resurrecting dragons.
- Legend says he will destroy everything
- Lots of Dragons are harder to kill than 1 elf.
- Only the Dragonborn can slay a dragon, let alone the strongest of them.
- Dragons are actively burning down towns throughout the game.