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?
Namor - Not currently in a series (ok, his LS just started). Had that run-in with Super Skrull aka 'Iron Fist' years back, and had his memory erased right after.
Stark - Too much of a copout. Hope not.
Reed Richards - Stretchy powers? Easiest to replicate. Super science and exploration scarily explained by advanced civilization scouting potential targets. Conspiring with Lyja? Eep, what about his kids?
Black Bolt - Most obscure member of the group, most time offscreen to do stuff. Always moving Attilan. Never talks. Very suspicious.
Dr. Strange - Least likely, due to Sorcerer Supreme complications. And yet, Avengers Disassembled, House of M... Nah...
Professor X - Most likely. Always going back into space to hang out with Lilandra. Telepathically verifying what others are saying is true. Anyone remember Maximum Security? He was training a team of Skrulls, for goodness sakes!
Black Panther - Okay, so he turned down membership. But with all the discrepancies due to the relaunch of his series, I really hope Skrulls can be inserted to make sense of it all.
Other likely candidates: Sentry and Jessica Jones. Continuity implants, very recent and prominent.
DH the Lurker
(See! This is why we need Cosmic Avengers!)