Here's my long, random and probably lore unfriendly theory on the Alduin-Akatosh relationship.
So Akatosh was one of the original Gods, and was rumored to have mingled with dragons sometime before they disappeared from Nirn. Alduin is "the world eater" who the Nords believe both created and destroyed the world. I believe that these two beings were once separate, but became the same during a conflict between them.
My theory is that Akatosh was originally a purely human God like the other eight Divines, and Alduin was just an immensely powerful dragon whose strength was great enough to destroy the world. Akatosh, being the patron of invincibility and endurance, took issue with Alduin, the bringer of destruction, but was unable to destroy him. Instead, he fused with Alduin and, being a God, subdued the powerful dragon and sealed him within himself.
Since that time, crisis after crisis has weakened Akatosh, who aided humans in battling many powerful threats. His power finally faced it's greatest decline when Martin Septim shattered the Amulet of Kings and used Akatosh's strength to defeat Mehrunes Dagon. With Akatosh weakened, Alduin has become dominant over him, and has returned to Nirn with his dragon army to finish the destruction of the world.
If you've seen images of Akatosh (like the one below) you know that the God is usually depicted as being about 90% human, except for that weird vestigial dragon head linked to his own. That head is Alduin, subdued and weakened, but still in a sort of parasitic relationship with Akatosh. In Skyrim, perhaps the appearance is reversed: a massive dragon with a tumorous human head growing out of it.
Perhaps they even speak simultaneously, which would explain Todd Howard's comment that some dragons speak English: it's just Alduin speaking through Akatosh's human head.
http://images.uesp.net//thumb/2/22/OB-Window-Akatosh.jpg/250px-OB-Window-Akatosh.jpg
Anyway, it's a long crackpot theory, but I like it. I'm sure Bethesda has something cool in store, and I hope Alduin is as terrifying as I imagined him being here.