Alright, so it's Skrulls... so lets assume they've infested themselves in key places, where might they be?
I'm sure the X-Men will be involved in some way, but none of Whedon's team will be a Skrull and I doubt the New X-Men would have one, but it's possible.
I don't think any of the ongoing solo heroes have been replaced.. they did that with Wolverine a few years back and it cheapened the stories (it also meant every issue by Larsen did not technically have Wolverine in it).
It's not Maria Sharpe because, well, that would change the meaning of Civil War, wouldn't it?
Also, don't assume that just because we've seen internal monologue it isn't a Skrull. On multiple occassions the Skrulls have brainwashed their own operatives.
I doubt any of the Thunderbolts have been replaced.
So... here's my list:
Maria Hill - yes, it's the obvious choice, but at least one high-ranking official needs to be obvious.
Baby Cage - well dur.
Wonder Man - I'm thinking some time between the PAD series and Mighty.
Trauma - yes, it may be obvious because he has shape-shifting powers, but he's also the one with the least backstory in the Initiative.
Justice - he always wants to know what's going on and puts up just enough of a fight to seem displeased, but he always does as he's told and keeps secrets anyway.
Ditto from She-Hulk - wouldn't that be a trip? Okay, probably not.
Iron Man - I really want Tony to be a Skrull... not because I want to negate Civil War, that was all Tony, but because it would be the biggest coup the invaders could possibly make. It can't be him, however, as he's too central to World War Hulk right now.
Villains - I would not be surprised if a lot of villains have been replace (because seriously, who would think to check?!), and hey, Punisher just freed up a bunch of identities!
Who's on your list?
It can't be Wonderman or many of the Mighty Avengers for that matter.
Remember when Doctor Strange cast the spell to bring up the Mighty Avengers worst fears....
Well I doubt a Skrull would be scared of Simon's brother... for instance.
Dunno if a Skrull would be scared of the Brood - like Carol was...
A Tony Skrull....? Nah - I really doubt that...although he might be worried about a Dead Captain America I guess.... but I doubt it.
If a Skrull was in the Mighty Avengers then the fear would have been - being found out.
If any of this lot turns out to be Skrulls then Bendis better come up with a good reason for these Skrulls thinking this way.
My money is on Mr Fantastic... although I can't see why it would be during the Kree / Skrull war... I mean that'd make Franklin a half Skrull...
Also where are the people that the Skrulls took the form of ?
Captain Marvel stands out as the dodgiest resurrection.