Alex's father and Pyramid Head. SPOILERS

[paladin181]

In my view,
It's blatantly obvious that the bosses represent the children who were sacrificed by their parents:

Joey loved his tree house and his father buried him alive, hence Sepulcher being represented in the form of a giant tree like structure.

Scarlet loved dolls and I think it's suggested that Dr. Fitch slit her throat, hence the reason he would be cutting himself to atone, Scarlet takes the form of a giant porcelain doll, somewhat sexualized which leads to question her father's "relationship" with her.

Fitch flayed Scarlet. He skinned her and disemboweled her alive, not simply slit her throat. The knife method of death is one of the more horrific for the person performing it.

As for the rest of your take on the story, it does seem mostly sound.

[Soulless-Shadow]

Scarlet also has breasts. Why? I don't know. I've read some stupid theories, about her relationship with her father though.

Fixed for you.

lol I was trying to be nice, but you're right in fixing my sentence.

Fitch flayed Scarlet. He skinned her and disemboweled her alive, not simply slit her throat. The knife method of death is one of the more horrific for the person performing it.

Wow, I did not know he flayed her as well. I knew/figured he dismembered her, but I had no idea about the flaying. Poor guy... No wonder he went a little crazy....

[jeremyjh]

Interesting I always thought that the Pyramid Head resembled Josh since he killed his dad (as did all the bosses in the game that killed their parents) and on top of that when ever you went looking for Josh and he ended up missing you had found Pyramid Head.