Secret Invasion is back in the conversation thanks to the upcoming MCU adaptation. The 2008 event by writer Brian Michael Bendis and artist Leinil Yu was years in the making, with set-up stretching back to 2005's New Avengers #1. Marvel's ads for Secret Invasion got audiences everywhere excited, as fans questioned which of their favorite characters were going to Skrulls.
In the end, Marvel played things pretty safe with their Skrull imposters, unermining a lot of the audience discourse. Considering how much Marvel hyped up the event, fans actually accepted the idea that the heroes they came to know and love had been body-snatched (or were never themselves at all). Making heroes like Iron Man or Cyclops Skrulls would have elevated Secret Invasion to genuinely legendary status.
1 Emma Frost
Emma Frost was a controversial X-Man during her early years with the team. Fans hadn't really warmed up to her yet while some felt her tenure as a hero simply wouldn't last. Emma quickly took a place of power in the X-Men, and would have been a great target for the Skrulls. In fact, the Skrulls actually tried to fool the Avengers into believing Emma was among those they had taken.
The Skrulls mostly ignored the X-Men, though, which is pretty strange. Mutants weren't an especially powerful force post-House Of M, but the team was still an important part of the superhero community. Making Emma Frost a mole would have been perfect.
2 Radioactive Man
The Thunderbolts got a big push post-Civil War, becoming an important part of the superhero national security apparatus. Led by Norman Osborn, the team actually played an integral role in the battle against the Skrulls. The Thunderbolts survived an attack by the Skrull impersonating Mar-Vell and were the tip of the spear against the invading aliens, as the Avengers were still trapped in the Savage Land.
The Skrulls had no one among the Thunderbolts, but the perfect subject was right there. Longtime villain Radioactive Man had joined the team. Hidden in a radiation suit, he wouldn't have been difficult to impersonate. No one would have expected it and his powers would have wreaked havoc on the 'Bolts.
3 Wolverine
Unlike most of the X-Men, Wolverine was neck deep in the battle against the Skrulls from the beginning as a member of the New Avengers. Replacing Wolverine would have taken a lot off the Skrulls. He's an implacable foe, someone who will keep throwing himself at his foes and their plans. Taking Logan out of the equation would have made things much easier.
Controlling someone like Wolverine would have given the Skrulls a way to throw out false leads. Wolverine's sensory powers didn't detect the Skrulls, but they could have pretended they did, allowing Wolverine to finger false Skrulls and spread even more division. It would have worked like a charm.
4 Invisible Woman
The Fantastic Four were the Skrull's first superhero enemies. The Skrulls hated them more than any other superhero team, which is why it's so strange the Skrulls mostly left them alone until the battle got underway. Post-Civil War, Reed Richards and Sue Storm had left the team to work on their marriage, leaving Storm and Black Panther in their place.
This would have been the perfect time to replace one of them, and Sue Storm would have been the best. Invisible Woman is the most powerful member of the Fantastic Four, the Skrulls had experience replicating her powers, and she would have made a huge difference in the battle. Plus, it would have hurt the FF, which the Skrulls were all about.
5 Nick Fury
Nick Fury can be rather untrustworthy and manipulative, which is why he was in the perfect position to strike back against the Skrulls during Secret Invasion. He dropped out of the world after the truth about his attempted coup in Latveria was revealed. He used this time to build a new team – the Secret Warriors – and learn more about the Skrull invasion.
However, the Skrulls just letting Fury off and never trying to find him is a mistake they shouldn't have made. The Skrulls were basically in charge of SHIELD and already had Dum Dum Dugan. They could have taken Fury before he left SHIELD and had a powerful card to play against the heroes.
6 Captain Marvel
Captain Marvel's rise to the A-list was still underway during Secret Invasion. Still going by Ms. Marvel, she was field leader of the Mighty Avengers, a job that put her in the upper echelons of the Initiative. This made her a perfect target for the Skrulls. Carol Danvers had connections to everyone, from the X-Men to SHIELD, and would have made a great mole for the Skrulls.
The Mighty Avengers team had no Skrull members, which makes no sense. The New Avengers had Spider-Woman, so it makes sense for the Mighty team to have one. In fact, the Skrulls could have used Spider-Woman to lure Carol to imprisonment, since they were good friends.
7 Spider-Man
Spider-Man is Marvel's top hero, holding more solo books than any other character in the company. He's the company's flagship character, which is why replacing Spider-Man with a Skrull would have been such a great idea. He was the one hero no one would have expected being taken over by a Skrull; he's not exactly powerful and, at the time, was coming back from the havoc Civil War wrought on him.
It would have been a massive shock to everyone if Spider-Man was a Skrull. It also would have fit with the classic Parker luck that defined the comics for decades. Spider-Man being taken by the Skrulls is exactly the sort of thing that would happen to long-suffering Peter Parker.
8 Ares
Ares became a member of the Mighty Avengers post-Civil War, slotting into the powerhouse god role that Thor and Hercules before him had filled. He was fierce in battle, providing exactly the kind of muscle the team needed, but Ares wasn't exactly a well-known member of the superhero community at the time. In fact, he was mostly known for working with the Zodiac, a bunch of D-list villains.
Making him a Skrull might have been a little obvious, but it would have been devastating. He was not only powerful enough to beat most of the Mighty team on his own, but he spent a lot of time in Avengers Tower. The damage he could have done would have been significant.
9 Cyclops
Cyclops is a legendary hero, having led the X-Men against the worst imaginable threats. During Secret Invasion, the X-Men were at their lowest point, but still were a powerful team. They were also mostly overlooked by the Skrulls. Replacing Cyclops with a Skrull would have been a gambit that paid off well for the invaders.
The Skrulls went after very few actual high profile targets, so getting Cyclops would have been huge. He would have kept the X-Men tied up in a myriad of ways, and could have facilitated a full scale takeover of the time by Skrulls. It would have given the Skrulls a massive leg-up in their war.
10 Iron Man
Iron Man has many momentous milestones to his credit, and was the Director of SHIELD during Secret Invasion. Tony Stark was the top of the pyramid and should have been a prime candidate for the Skrulls. At the time, many readers actually speculated that Iron Man was a Skrull, as it would have explained his behavior during this time period.
While Iron Man definitely did a lot of damage without being a Skrull, replacing him would have been a coup. The Skrull already had control of SHIELD, so getting the Director would have been icing on the cake. Plus, Iron Man doesn't have any powers to copy to speak of, making this one a snap.