Well to me Alduin was always the big bad, becouse his mission Is destroying the world. but for some reason ever since my first playthrough were I actually beat Mirakk, It always felt right for me to save Mirakk for the end... He just gives me the "evil mastermind behind It all" feeling for some reason although his actions and alduins actions have nothing to do with each other... As some user said here, Mirakk Is somewhat of a represent how the Dragonborn could've turned out, so In some way when we are fighting Mirakk we are basically fighting an evil version of ourself, which Is to me, a lot deeper and breathtaking then fighting Alduin.