Well, this concept is not the most original, not anymore. This would probably have been super popular during the earlier days of Newgrounds, but I don't know today.
The animation is well made, the choice of sound could have been better in my opinion, some got repetitive and others are over-used, audiobank stuff. Now I would like to point out that there is a good amount of the animation that simply doesn't contribute to story progression in any way, and that is something that should be avoided in every work driven by a plot. It makes it longer and dull to watch, and it's also more unecessary work for you.
Now, about the story per se. Well, like I said, it takes some time to get to the point. And with time, all of this "cute things suffering" gets overdone, there's too much of it and it stops being interesting after a while. Also, I had the sensation that it was a bit shallow due to the fact that all of this violence had no point at all, actually, it was the point, the whole story progressed to a bunch of little cute things suffering. You may notice that everything that offers ultra-violence does it with a purpose, there's an excuse for all that blood and gore, even if it is a bad one (take a look at Happy Tree Friends, South Park). But like I said, this would have been golden on the earlier days of NG, free violence was popular here back then (see Madness), but now? Not anymore.