With the confirmation that Captain Marvel will be set in the 1990s and will feature the MCU debut of the Skrulls, talk has inevitably turned to the possibility of Marvel's seminal story event Secret Invasion being the next big MCU arc. Just imagine the impact of a direct transition from Thanos' attempt to crush the universe to an even bigger threat... It would change everything.
The best way to do it would be to have Captain Marvel explore the Kree/Skrull War and reveal the Skrull intention to invade Earth without showing specifics, and then to have the secret invaders teased in the background to the culmination of the Infinity Arc in Avengers 4, perhaps with a pay-off reveal of a big character being an impostor. Now that would be a hell of a way to kick off Phase 4....
So who would be the best candidates to be aliens in disguise?
11. Tony Stark
If Marvel do choose to go with the Secret Invasion storyline, there's no point in doing it half-baked. Kevin Feige has already talked up Avengers 4 and beyond completely changing the MCU, and it's time to start making some deep cuts. What better way to announce that sort of change than to mess with some of the pillars of the franchise?
Inevitably, any major twist would probably inspire the same sort of fanboy rage that met with the reveal of Captain America being a HYDRA agent in the comics, but that's arguably the whole point. Just imagine how much impact having Tony Stark be a Skrull would have.
It wouldn't even be that difficult to write Tony's ideological stance against unregulated superheroes as a hint of his infiltration, or his PTSD as the Skrulls means to catch him off-guard and replace him. It's an easy thing to write, and it would come with the advantage of ensuring the Avengers couldn't simply rely on their genius inventor to come up with a way to detect the aliens.
As an added bonus, revealing Robert Downey Jr's Stark to be an impostor would allow for an opportunity to recast him (assuming he actually wants to retire). And continuing the golden Iron Man brand in the MCU has got to be considered good business.