MCU Secret Invasion: Which Heroes Could Be Skrulls?
7. Pepper Potts And Happy Hogan
If Marvel don't choose to have Tony Stark revealed to be a Skrull, the next best thing would be having him surrounded by influences who could be seen to be guiding him towards the Skrulls' agenda.
And like Falcon representing a good choice because of the impact he would have on Cap, either Pepper Potts or Happy Hogan (or even better, both) would also bring that entire story arc back round on Tony. He was, after all, blinded to Cap's sympathy for his friend Bucky because of his part in the murder of the elder Starks, and there's a delicious opportunity for irony in Tony discovering that his closest companions are legitimately evil impostors.
They could also be introduced as having manipulated Tony's mental state to cloud his judgement and his ability to function as a superhero, as a long-play agenda to rob Earth's best line of defence of structure. And again, it's about time Pepper Potts was given something of substance to do.