Such a reveal would have us rewatching past movies and investigating like a game of Clue, steeping the MCU in a pervasive sense of paranoia. To build a new world you have to burn the old one down, but the Skrulls could have simply been redecorating while we were distracted by Thanos. Rather than being a physical threat a la the Mad Titan, this kind of infiltration would be more cerebral, similar to what we saw Hydra do to S.H.I.E.L.D. in Captain America: The Winter Soldier, which effectively crippled the MCU organization.
After all, the Skrulls are prominent villains in the comics, so we can't see Marvel just wiping them out or jettisoning them into deep space, never to be seen again, without leaving some lasting damage. They could be the first wave, with an empire soon to come. After the presumed defeat of Thanos and the restoration of the universe, this looming threat would certainly cast a dark shadow on the heroes trying to recover (and avoid more cosmic damage). This would even give agency to the likes of Nova, new Guardians and maybe even S.W.O.R.D., truly ushering in a new era for the studio.
Guessing who's a Skrull and how deep they're embedded in society is something that could be a common denominator across all future movies, uniting them the same way that Thanos' search for the Infinity Stones did over the last six years of the MCU. A Secret Invasion-influenced phase of films would offer the same emotional heft, mentally taxing us by providing plenty of fodder for post-credits scenes and in-story mysteries.
What makes this all the more intriguing is that it could even introduce the Fantastic Four, as they were the ones tied to the Skrull's first invasion of the planet. In 1962's Fantastic Four #2, the Skrulls scouted Earth via a team of four, sent down from a mothership floating in orbit to clear the playing field for a full invasion. Their plan involved transforming into the Fantastic Four, tarnishing their reputation and ensuring Marvel’s First Family was so badly off that they couldn't assist in thwarting the alien invasion. The Skrulls succeeded, kidnapping the Fantastic Four along the way, but ultimately the heroes emerged victorious.
Phase Four could use the Fantastic Four as the main party investigating the remaining aliens, adjusting this storyline to suit. They're known for their galactic adventures after all, so this puts Reed Richards and company in the limelight, reminding the Avengers that the job never stops. Not to mention, the Fantastic Four and select Avengers working like a group of science detectives is something all comic fanboys are waiting to see. With that in mind, we first have to see what Captain Marvel has in store for the green-skinned aliens, but that doesn't mean we shouldn't hope for a grander role once Carol Danvers takes the Skrulls' first mission apart.