Honestly; why I love how Skrulls are handled, is because it sets an example of not judging EVERY group of Skrull's as the enemy. It sets the space (pun unintended) to allow Marvel to flesh out the Skrulls, to establish different factions, mentalities, and beliefs. It could even set the stage towards a Secret War, set across multiple films and without needing to be apart of one giant film. Will there likely be Skrull's who do stray into the darker, more evil path? I would assume so, especially if Captain Marvel decides to go and give root to showing that.