There are lots of reasons to be excited for the upcoming Captain Marvel, but one of the subjects that has gotten a lot of focus -- other than Captain Marvel punching an old lady -- is the Skrulls. The shape-shifting aliens will be making their MCU debut in the movie as the antagonist, with Captain Marvel stuck in the middle of their war with the Kree. Since the news of the Skrulls' involvement first dropped, people began theorizing that other MCU characters would be revealed to be shape-shifters all along. As cool as those theories are, that comes with a massive problem because it makes significant character development potentially pointless.
A little extra context is in order. The Skrull were first introduced in 1962 and have primarily been enemies of the Fantastic Four, though they have troubled other heroes as well. Their main power is the ability to shape-shift, but they later learn how to genetically alter their warriors to have the same abilities as Earth's heroes. Perhaps their most prominent story is Secret Invasion, in which it's revealed that the Skrull have replaced several significant figures on Earth in a long-term plan to take over the planet. The heroes already didn't trust each other because of Civil War, so a complication of this scale wasn't helping matters. It was a vast comics event that crossed over dozens of different series, and it would make for a fascinating movie arc.
But that doesn't mean it can be entirely translated from page to screen. The main problem with these Skrull theories in regards to the movies is that you can't replace a main character like Iron Man for the long term because that means that anything you watched them do during that time has no meaning.
So let's lay out a hypothetical situation. It's revealed in an upcoming Avengers movie that Black Panther was replaced, and it's actually Skrull Panther that we've been following since the end of, let's say, Avengers 4. In this scenario, that means that we've likely gotten Black Panther 2 and seen T'Challa overcome some obstacle and go through some character development. At the time of watching this movie, we don't know he's a Skrull. However, Avengers 5 drops the bomb, and it's a huge twist. Maybe it's executed well in the movie, but it doesn't change the fact that whatever happened in Black Panther 2 doesn't matter now because T'Challa didn't go through that experience. That retroactively damages the sequel.
What I just laid out is a pretty specific situation, but if people want main characters to be Skrulled, then there are limited options. That's not to say that there aren't ways to get it to work. For example, they could tease during Black Panther 2's end credit scene that T'Challa gets switched out with a Skrull, and then hint that something is up with him during the lead into Avengers 5. That keeps what happens in the sequel meaningful while keeping the Skrull twist intact. It's called having your cake and eating it too.
It's also important to remember that during the Secret Invasion storyline, there weren't any big name superheroes who were replaced. The biggest were Hank Pym, Spider-Woman, and Jarvis the Butler, while others like Iron Man, Spider-Man, and Wolverine were left untouched. I would imagine that bigger names weren't revealed to be Skrulls for the same reason I listed above: it would just make everything that happened to that character prior pointless.
There's nothing wrong with only replacing side characters though. It's still an effective way to create a twist, and it dances around the character development issue because these guys don't get much anyway. For example, Selvig, M'Baku, or Maria Hill would make decent choices, or if you want a bigger wallop, then any Avenger without a standalone movie would do. The theory about General Ross being a Skrull is excellent because he's not a pivotal character, but he's recognizable and in a position of power. He'd make an awesome Skrull, so more characters like that being potential Skrulls would be great.
There is an argument to be made that because the Skrulls aren't main characters, that means it isn't "meaningful," but that all depends on the execution. If the story and action are good, then people will be happy to go along for the ride. Of course, one main character could end up being a Skrull to help add some extra punch, but Marvel would have to be careful with how they execute that. Thankfully, Marvel has shown to be nothing but careful when it comes to the planning of their movies.
