A fair assessment and one good suggestion
The story was so so but I have always felt Newgrounds is a forum to show of you animation/flash abilities foremost before anything else. And your anmation is not too bad you have shown improvement with each episode and I think if you continue you work you will be an excellent animator.
If you are concerned bout story telling with this project I would say I saw numerous points in which you could have had plot twists and whatnot to really take this good guy must stop villian reads like any Zelda game story into something so much more.
I would suggest taking that basic idea and stretch, push, pull, even perhaps take from it...manipulate it to the point it becomes so different your basic ida is completely lost. Then take one step back. (perhaps another if you wanna make sure your underlying idea is clear) Then your good guy villian story is there but the idea has been manipulated in a manner that it isn't obvious and just like you pulled a stock story out of a warehouse.
So to all you idiots trying to sell your writer abilities over ah rating system thing STFU and go to Monsterjobs to get work. And help the man with his work by giving tips and ideas not by just saying come to me.
Also people who are wondering about the end...HOW'D YOU MISS THE TYPICAL" AND EVERYTHING GOES TO THE WAY IT WAS BEFORE AND THE HERO GOES TO HEAVEN OR SOMETHING LIKE IT."