1st a little basic history lesson about Akatosh/Alduin. He is the Chief God of the Nine Divines and the deity that St. Alessia got the Amulet Of Kings from. The Amulet is made of Dragonblood, its Akatosh's blood as he took pity on the humans and crafted the Amulet to keep the Daedric away. Also he gave the humans the Dragonfires which would always be lit as long as there was an emperor who was of the Bloodline of Alessia who wore the Amulet, the Gateway to Oblivion wouldn't be opened.
Next the Events of Oblivion which caused the real main problem which is going to hopefully be addressed in Skyrim. Mehrunes Dagon wasn't happy as he wanted to conquer Tamriel and he truly believed that Nirn was his plane. So he came up with a plan, The Jager Tharn plot was the 1st part of his plan but it failed because Tharn couldn't persuade his Protege to join him which lead to the Hero of Arena getting the Staff Of Chaos and stopping Jager Tharn. So Dagon had a better idea kill the Emperor and his heirs hearby getting rid of the Dragonfires and allowing the gates to Oblivion to open. He succeeded thanks to Mankar Cameron and the Mythic Dawn. However unknown to Dagon and his allies a lone prisoner, The Hero Of Kvatch would hear the call of the Emperor and stop him. In short it lead up to the Hero finding the last and lost heir Martin Septim and getting him to relite the Dragonfires and stop Dagon but that didn't work. Dagon had already crossed into the plane of Nirn and would start his conquest of it. Martin then made the decision to smash the Amulet of Kings and become the Avatar of Akatosh. Which that worked it destroyed Dagon and save Tamriel from Dagons wrath.
Now your probably wondering well why does it matter what happened in Oblivion, well it does matter because Martin broke the Pact that St. Alessia had with Akatosh. By destroying the Amulet Of Kings Akatosh is free to act on his own and by seeing what the Mythic Dawn did to the Emperor and his 3 sons my theory is that Akatosh/Alduin is unhappy with the way that people act and I believe that he see's evil everywhere and Alduin thinks that it's time to recreate a new plane. My belief is that he will use the Cult Of Akatosh/Alduin to start the process. They will go by a different name which I can't really theorize because it could be anything. Also if a new plane is created everybody will probably die on the current plane that's my theory at the moment. That is probably the best reason as to why Alduin is the Antagonist in Skyrim. Your the last of the Dragonborn which are descendent from Alessia. I believe that the Protagonist will be the only one that can stop Alduin but how you stop him well that will be revealed when your playing the game.