And the whole "The massive country with loads of money, a strong council that was stronger that the emporer, a massive army and proof that their god favors them falls apart because their Good Emporer died and that's all that matter."
Yes it does, since it didn't happen that way. The Good Emperor was the vital link with this god or gods, otherwise the whole scenario with the amulet of kings becomes worthless. No one else actually saw the dragon do what it did, and few people knew who Martin was. If anyone saw everything, it was Ocato, and we all know he's a bit useless.
I wouldn't take it as a sign that Akatosh favours whoever more than anyone else. Every culture has experiences of the gods, Aedra or Daedra, and every nation in Tamriel has a religion which expresses this in at least in one form or another. Martin's sacrifice saved all of Tamriel, not just Cyrodiil and it's awfully pious citizens.