Alduin is Akatosh. Same god, different name. I'm not the expert on it, though, and that's only my understanding of Alduin/Akatosh. And, as Alduin is the main enemy, it can be assumed that the dragons do work for him.
No, no one knows what Alduin is. Anyone who says they know who Alduin is for sure and know his motives is just guessing. There is only one piece of lore that equates them and that was a loose association by a mortal author. People going around spreading misinformation as fact when it isn't really get under my skin.
To be more specific, it's just the way things go. Akatosh creates the world, and Akatosh destroys the world. The time has come for this world to end so that Akatosh can create a new one.
Well Akatosh didn't create the world. Magnus was it's architect, Lorkhan thought up the very idea of the world and the mortal races and the aedra (which include Akatosh) sacrificed large amounts of their power and even some of them gave up their entire beings, to make Mundus. Akatosh didn't create the world by himself and there is no evidence that Akatosh is going to destroy the world and remake it, especially since it took so much out of the Aedra before to make the world, how would they remake it again? That's not even including the fact that the mortal races worshiping the Aedra are what gives them their power, why would they kill those that give them power?