Considering Secret Invasion's status as one of Marvel Comics' most landscape changing events to date, it's understandable why fans believe we'll eventually see a version of it in the Marvel Cinematic Universe, albeit with a few tweaks. The event completely changed the status quo of the Marvel Comics universe, and there's no doubt it could do the same for the MCU.
Changing things up so drastically in the wake of Thanos' threat, however, may prove harmful to the established MCU. The Mad Titan shook things up in a major way when he dusted half of the universe in Infinity War, after all, so is it really a good idea to throw the heroes directly back into disarray, so soon after they (presumably) put things right in Avengers: Endgame?
The Skrulls Are Coming
The alien race known as the Skrulls are set to appear in Captain Marvel, with a spotlight being shone on their infiltration methods. This isn't the first time we'll see evidence of their MCU existence (their language appeared on computer screens as far back as Guardians of the Galaxy Vol. 1), but it will be a shock to the Avengers' system nonetheless when they eventually learn of their existence. The entire premise of Secret Invasion is that the shapeshifting and infiltration acumen of the Skrulls makes it so that no one can trust anyone, so you can understand why Marvel may want to explore this direction. It presents a risk, however, given that we've already seen the mistrust angle not too long ago, in Captain America: Civil War.
Things in the MCU currently appear to mirror the environment the Secret Invasion occurred under in the source material. Knowing fans have been talking about this, Captain Marvel's producers even addressed Secret Invasion rumors, saying they's "always" planting seeds for future films. And considering how fractured the Avengers have been ever since Civil War, even if they do end Thanos' threat in Endgame, the heroes are still vulnerable to another, even more insidious threat.
A Changing of the Guard
With some of the films' longer-running stars apparently set to depart after Endgame, new figureheads will be needed to carry the Avengers torch. While it is hard to imagine the MCU without the likes of Chris Evans or Chris Hemsworth, this will eventually be the reality of things. With the grand plans Kevin Feige has for the future, relatively new heroes to the MCU, such as Black Panther and Captain Marvel, will need to be built to the same level as Captain American and Iron Man before them.
The problem is, if they pull the trigger on Secret Invasion too soon, it may make these newer heroes hard to invest in. It would be pretty jarring to follow, say, T'Challa for another film or two, only to have him be revealed as a Skrull, forcing us to get to know the real character. And it has to be a big gun on Black Panther's level to make it work, as revealing, say, Everett K. Ross as a Skrull wouldn't have a heavy enough impact.
The Slow Burn is the Best Burn
The reason Infinity War and the upcoming Endgame has fans so hungry is that the build to the story was gradual and meticulous. Details being dropped across all films for several years makes the payoff all the more sweet, and helps reinforce the idea of a living, breathing narrative universe. If Marvel approaches Secret Invasion in the same way, it could do something really spectacular. With after-credits scenes no longer locked in to teasing Thanos' quest for the Infinity Gauntlet, suspicion regarding Skrulls could be sown with these scenes instead
With Disney's recent acquisition of Fox's Marvel assets, there is time to build to the Skrull infiltration of Earth's super teams over several phases, much like it did Thanos' threat. It would give Marvel time to bring the X-Men and the Fantasic Four into the fold, if desired. Having the invasion affect a number of super teams, as it did in the comics, would give the event the gravitas it deserves.
To really deliver a Secret Invasion to capture the chaos Skrulls can cause, the timescale on the story needs to be expansive. Fans of the MCU will need time to get fully invested in the post-Endgame reality, as things will likely change drastically. The Skrulls need to be portrayed as a formidable, looming and powerful threat, and suspicion of their whereabouts within the MCU needs to reach fever pitch in order to earn the best possible pay off.
Secret Invasion was an incredible story that relied on a lot of groundwork and backstory. There's little doubt Feige and co. are capable of putting the time in to make it something grand, but with the Kree/Skrull war arc seemingly being condensed into one Captain Marvel film, there's reason to worry about this being too abrupt as well. Secret Invasion is the kind of story that needs time to breathe, with attention to creating an atmosphere where no one can be trusted. Here's hoping we're still piecing clues together throughout Phase Four, and well into Phase Five.