The Shi'ar and the Brood

Only Talos' unit of Skrulls have been shown to not be evil. Feige has emphasised this.

Something I really appreciated about Captain Marvel was that it didn't paint whole races with one brush, like most space sci-fi does. The Kree have different skin tones, and different attitudes - some are better than others. These Skrulls perhaps have bad members, and admit to having blood on their hands too, but aren't necessarily bad. Other Skrulls may be evil. The races aren't one thing.

@BEJT That's a fair point. I agree. It's is really nice seeing non-human cultures that are just as complex as human ones.

Feige's quote:

"I think like the Kree and like humanity, there are good Skrulls and there are bad Skrulls. But one of the things we wanted to do in this movie is, you know, don’t judge a book by its cover and tap into people’s preconceived notions of the pointy-eared green aliens being evil and subverting that. But I do think to continue fleshing them out and making them these three-dimensional actual beings, the Skrulls, you would encounter good ones and bad ones."

^^ exactly. Don’t consider what the MCU did to be “flipping the script”. There are going to be noble and sinister sides in each war, especially one as complex as the Kree-Skrull.

For every Mar-Vell, you’re going to have a Ronan or Yon-Rogg.

Same thing with the Skrull: for every Talos, you’re probably going to have a Veranke.

And as for OP’s other question, I’d love to see the Shi’ar and Badoon. Maybe the Phalanx and Brood, too, but much later on.

They couldn't replace the Skrulls for a Secret Invasion storyline, unless there is another shapeshifting alien race out there that I don't know about.And as others have said ^^^ there are Skrulls who are bad, so if the storyline ever happens, they will likely use them. However, that then raises the question of how will the MCU good Skrulls play into the story, as I don't recall there being good Skrulls in that story, so that'll be interesting.

Secret Invasion won't happen.

^It will happen eventually. And actually it can be the next big arc by the looks of it.