Oh, Emma won't be Otacon's sister??
She won't be E.E ? That sounds horrible. I thought it'd be just a different succesion of events..... then now that's what explains Meryl's presence there..... so the story will be completely different, I'm afraid.
Now let's just hope that Kojima won't do the same thing with MGS 3..... Raiden as the protagonist, and then he'd release MGS 3 Substance