I have formulated a theory concerning Akatosh, and his role in The Elder Scrolls series. I have created this idea, of an above average understanding of the lore, but I am no expert. This theory is also based on the idea that "In the Elder Scrolls series, we have of arcs over multiple games, Oblivion ended the first major arc, and Skyrim began the second."
Let's look at the beginning, there are a couple of creation myths, but I will be settling with the one where the Aurbis created the et'Ada, which after Lorkhan's deal became the Aedra and Daedra. Lorkhan tricked a few of the et'Ada into helping him build Mundus, for this they gave up their complete immortality, those who helped build Mundus became the Aedra, those who refused became the Daedra. So that being said, Akatosh (and the other aedra) are bound to be upset with Mundus existing, seeing as that its holding them back. Akatosh is the only one openly doing anything about it though, he created the Alduin to consume the world, and created the Aldmer to rule it. He gave the men, a hero, who could force their worship to dragons, he gave them Miraak, and the ability to bend the will of mortals. But it was Hermaeus Mora who gifted Miraak the ability to rebel, and the men followed this example and they also rebelled, sending Akatosh's dream child into the future. After Mora's interruption with the mortal world, which lead to Akatosh's first downfall, Akatosh gave men the dragonfires, to keep the Daedra out of meddling in such ways. Akatosh was worshiped by all for his generosity. Then the Oblivion crisis came, and Akatosh had time to make his move, upon destruction of the Amulet of Kings, Akatosh ended Septim bloodline, allowing the elves to go forth with his plan. The empire broke, and the tower fell, during the great war, tower after tower would fall, with the most recent being the snow tower, via time wound. Upon alduin returning to time, Akatosh bestowed the Dragon Blood, one final time. Why only one more time? Because that's all it takes, if the current Kalpa had ended, Akatosh would have had to start fresh.
What does Akatosh plan to do, its simple, he is sending the Elves to destroy all the towers holding Mundus together. The Thalmor are doing this and masking it as a holy war. Akatosh wishes to unravel Mundus, and unbind himself from his deal with Lorkhan, he wishes to do this now, because he has lost all faith in the men. Essentially Akatosh wishes to become a Daedra (and possibly force the other Aedra into becming Daedra).
I guarantee I got some of this wrong, and there are conflicting myths, and stories.