Very Nice idea.
Even better: before joining Alduin, and to prove your worth, you have to subdue the Dragon Priests, the 8 of them and then obtain Konahrik, proof that you are now the "Anti Dragonborn" and pledge allegiance to Alduin.
After that, you will have to "conquer" each hold, beginning by the small one, to place one Dragon Priest as a "Jarl" in it. In Winterhold, you will have to destroy the College. In Whiterun, Help the Silver Hand to destroy the Companions, as there will be a Silver Hand questline that pops up. In Falkreath, either destroy or make the DB your own. Same in Riften for the Thieves Guild. Obviously, the Blades and the Penitus have to be gone too, as well as the Greybeard. 9 holds, 8 dragon priests and a Dragon Emperor (You). You can choose your Capital.
You would get dragon souls as a reward from "missions" given by Alduin, so you can activate the Shouts. You still only get 20 shouts though.
A "Civil War" will go on after you conquered 4 holds, the rest of skyrim putting their grudge aside and presenting an united front to take you down. They will have the Dragon born at their leader, that you will have to kill.
The game "ends" when you conquer all 9 holds and kill the Dragonborn in one on one combat, in an Epic fight.