I finally finished it, and I'm glad I did.
Disturbing in all the right ways, particularly in the forest area, though I also enjoyed the conversation with God. Some of His dialog was confusing, however, particularly when he said "3301 tried to warn you" -- due to the order I did things in, this was the first time I had even heard of 3301. (And indeed, the Archangel was the last puzzle I solved; I had assumed that he was a red herring for the entire game.)
There are a few things that I would like to know more about, such as the significance of the masked man, the dead bodies with numbers on their faces, and the rain of pineapples. And I do hope we get to see the unused content at some point.
However, for what we got I must offer my praise. One of the best things I've seen on Newgrounds. Do keep making more.