IMHO The Marvels has serious pacing and story issues. The whole Multiverse connection was weak and was also spoiled by the trailers. Secret Invasion connections were also weak and poorly constructed. The villain was weak. Supreme Intelligence is on the screen for like half a second and basically killed off-screen. We also should've actually seen the Supreme Intelligence in the first movie in the final act to expose its true form.
A more satisfying final act for The Marvels is Carol and her team all making a final push at Supreme Intelligence, and they are faced with the choice of if they should execute it or not, similar to Operation Galactic Storm. Ultimately, though one of the Kree rebels, maybe even Mar-vell who is revealed to be alive and leading a resistance on Hala, decides to kill it. The Kree at last take their destiny into their own hands and make a hard choice to lead themselves instead of relying on a totalitarian super-computer. Similar to the ending of the Kree War in Avengers: EMH.
Secret Invasion also makes no sense. If the Skrulls had a bountiful and safe new colony before this movie, why didn't all the Skrulls go there? And why did they all go back to Earth? Looks like the Skrull colony was doing well and thriving before Dar-Benn sacked it. And yet the Skrulls blame Fury and Captain Marvel for disappearing. When did they disappear? Carol went to Hala, destroyed Supreme Intelligence, and set up a new colony for the Skrulls. So she went to bat for the refugees.
It seems like Secret Invasion if you do it at all, should've been done AFTER The Marvels. Because then the Skrulls have motivation for resenting the humans, Fury, and Captain Marvel. They would be motivated to blame Carol for the destruction of their colony and the loss of their kin and to also make Earth their new home.