Well, for the mostpart many think it's just a different way of looking at the story. However, Konami pretty much fixed the lid on the story, implying that Maria was, (in the Silent Hill 2 story), just a ...

Spoiler:
Figment of his mind.


To be honest, I prefer the thought that she was...

Spoiler:
Made up

...To make James guilty for what he did to Mary. I don't really think he wanted Maria's traits, since he, in most of the endings, just wanted to his wife.

Unfortunately, it was too late, but I'd have liked to known that James had kept his wife in mind always.

You need to remember that Mary's illness disfigured her and caused her to have violent mood swings, so that's probably one reason as to why James was pushed away from her a little.