Now, a few people here and there have made some theories up on the recent added ending. Obviously, spoilers ahead for those who haven't seen it, though, so... careful. I'd like to throw my own out here:
The Issac we play is NOT the actual Issac, in any sence.
Run with me here: The first ending shows that Issac was busy writing the very first "Bible kills mom" ending down, and then BOOM, mom appears. Genuine supprise on the part of Issac there, but he has not crawled into the toy chest.
Then, the next 9 or so endings basicaly have him open the toy chest and find more and more stuff - not really 100% important to plot.
Then, we find the dead baby, and then, we see Issac crawl into the toy chest to escape the horrors of Mom.
Now, let's throw a theory out - What if the toy chest was written as well?
The final ending shows Issac looking into a mirror, seeing a demon, looking towards the toy chest, and showing genuine sadness. Guilt, perhaps?
What if the demon IS the real "Issac" that we play? What if the dead baby we play and the Issac we play are two different entites?
Let me try and run through a possible timeline:
1) The demon, or perhaps The Devil, convinces Issac's mom that he must be clensed, and eventualy sacraficed.
2) The True Issac hids away in his room, then in the chest, and (perhaps) eventualy suffocates - becoming the dead baby.
3) Meanwhile, the demon take the form of Issac, and starts to truly belive that he is Issac. Then, he comes across a book that The True Issac wrote in, in the time between being locked away in his room and realising he must lock himself away.
4) The demon reads the book, where Issac fights mom, himself, satan, etc. - seemingly from the same point of view as we play...
5) However, an unseen page then states that he was "killed" by a demonic self. The demon then realises that he IS the demonic self - That he is the reason that Issac is locked in the chest.
6) (Just a possbility here) The demon decides to sacrafice himself in place of Issac, and decides to write a happier ending - which is where the Epiloge fits in.
Admitidly, this is all guesswork. There are a few unanswered questions, such as why the demon would feel guilt in the first place, but I personaly think it fits, at least to a degree. Just wanted to throw another theory into the mass of them.