Enthralling experience
First, I really enjoyed how Skinny moved. It was so fluid.
Second, the atmosphere was so somber and post-apocalyptic, but at the same time it seemed familiar. The familiarity I think came from when Skinny woke up. The place was his home. It was a good mix of feelings, anyway.
Third, what really got me into it was the disturbing people trapped in their chairs. They would be so aware of what's going on around them, scared to death, and then when you would give them the batteries, they'd be so happy.
I think that was the penetrating point for me. The truth scares the fuck out of us. The fact that nothing is ruining our lives (both personal and as a race) but ourselves. The fact that we're really not so special can be wiped off the face of the Earth at any moment. The fact that the only lasting relationship we will ever have is with ourselves - we're truly alone in our heads. The fact that we have the illusion of choice underneath a tiny but potent upper class that we aspire to be like but to whom we will most likely never come close. Things like that.
So, to relieve the fear of reality, we block it out and focus on nice things like fishing, cookouts, family, friends (everything the people in the chairs would say after you gave them their batteries) hoping like hell that no one like Felix will come along and steal our comforting delusion.
Can you blame them, really?
Speaking of delusion, the most comforting and pervasive one in humanity's history is religion which you implied with the church scene at the end. That the church and Mama's lair are the same place means that you are specifically targeting religion (Christianity? It looked like it to me, anyway) as the delusion we're facing. And it makes sense as not only does Christianity give us the illusion of comfort (heaven and that we're loved no matter what), but it's also an excellent source of fear-mongering (hell, for example).
After the church scene, you enter into that crazy awesome looking chair thing which Felix calls, "The System." That's where Mama operates. It's where she controls her society. It's not too far of a stretch to see a parallel between the entrance to The System being inside the church and the entrance to delusional thinking beginning with religion (though in reality, I wonder if religion is the sole cause).
The real sadness in this, though, is not the masses' delusional thinking (though that is a big one...) but instead the misinformation the masses receive. The adults strapped in the chairs were worried about getting cancer, though it's clear that the two children running around were fine (at least the girl said she was). There never was any cancer. Similar to religion, this is a form of control. Mama personifies the human desire to have complete control. I mean, we really do like making things are way, right? I've backspaced a million times in this message making sure I don't mess anything up. On a bigger scale, when humans have power, they like to make sure nothing is messed up as well, only that usually means controlling everyone, fear being a favorable weapon. A nice test of this is looking at the sensationalist, conflict-obsessed media.
So when Skinny enters that last, unseen chamber, he's going to eliminate this control Mama has over his society. That's where the game's true fantasy comes in. If only there were one entity that we could destroy in reality that would end our self-imprisonment. But it's not that easy. You can't "kill" religion, fear-mongering, or our need to control. You can't kill attitudes. It might be easy to blame government, but if one government falls, human nature doesn't. We still like to control stuff.
There is no one supreme evil ruler (Mama) trying to control everything but instead our own nature. We really are fucking ourselves over.
That doesn't mean we can't try, though. Nothing will ever be "perfect," but they can be better. Also, we can try to escape our own self-imprisonment - the need to follow someone, the need to control others, paranoia, etc. And that's about all we can do, right?
Fantastic game!