The first season was good, but I think they went about it (and the rest of the series too fast) The villain in season 2 could have easily been swapped for the final season while keeping things similar.
Imagine: following Amon's cover about the spirits blessing him with the ability to remove someone's bending, despite being a bloodbender. He could have easily been one of Vaatu's pawns to break free. But failed and lost his bending forever thanks to Korra (and not have the lame ending that was given to him at the end of season 1)
They could have swapped things around with Korra's uncle, saving him for last while swapping things around with the villains for season 3 and 4. They could have easily been influenced by Vaatu to become his pawns by making the world unbalanced and while trying to keep Korra/Raava out of the way.
Vaatu as the series main villain would have been amazing for season 4, and we could have easily had the ending with Korra and Asami at the end as well.
But we got what we got. In the end the series was good, but it won't be as good as AtLA.