After Martin mantled akatosh, it took certain powers away from akatosh. After a couple centuries of rest, that part without those powers became alduin.
And maybe after both parts are destroyed (I'm assuming the martin/akatosh part was destroyed at the end of oblivion), then the two can become whole again.
I'm sure someones already thought of it, but its 6am here, and I haven't been to bed yet. Just kind of popped into my head.
Of course, I'm pretty sure alduin has little to do with akatosh, but this sounds more interesting than "he just exists".