Re: Secret Invasion: The End - SPOILERS!
^I can't help but think that someone like Mr. Sinister or Magneto might have taken her place if they were available, though.
According to Bendis, that's exactly what happened.
Quoted from WizardUniverse.com
Originally, it was going to be Magneto in that chair but continuity would have it where he just wasn't available and we all got together and Fraction was cool enough to let Emma get in there and, boy oh boy, that just makes her the most interesting person in that room to me. [The Dark Reign] special is actually written from her point of view mostly and I'm looking forward to it because that is a character that's kind of straddled both lines for a long time and now a hard decision is being made for her.
So it sounds like she may either be the weak link in the Dark Illuminati, or she might be in for a bit of character regression. I'd prefer the former, given the choice.
"Look for me by the moonlight, watch for me by the moonlight
I'll come to thee by the moonlight, though hell should bar the way."