****SPOILER ALERT***
So Flint was a butt pirate. Man what a waste of a season.
We already knew that Flint was gay. It was made very clear in season 2.
I thought the ending was solid. They did their best to keep the show relatively consistent with history. We know that the Pirates never gained control of Nassau, and that their way of life eventually died out. I liked that they showed that happening, while establishing that Jack couldn't give it all up and opted to continue doing what he loved. Of course, as Mega pointed out, they also established the "Treasure Island" origin.
I also liked the scene where Long John Silver came across the guy hiding in the hold of the ship like a coward. He was "just the cook", which was a replay of the scene with Flint finding Silver hiding in the very first episode.
All in all, I thought the show was really strong, until the last season. They ran out of interesting content and it was just betrayal after betrayal at that point.