MCU Secret Invasion: Which Heroes Could Be Skrulls?
5. Nebula
It's pretty key to consider the primary Skrull directive to conquer the universe: destabilisation is a major part of that, but it's also worthwhile considering the fact that the alien race would be very keen to monitor rising powers who could potentially make their own invasion more difficult.
What if they identified Thanos - himself a part Skrull according to canon - as one of those huge threats and ensured that they had a close representative in his midst to keep tabs on him? Since both Nebula and Gamora fit that bill, you could suggest either of them, but the blue fury is a far more compelling suggestion.
It would add another edge to her hatred of him, and her desire to destroy him, and it would explain her unwillingness to kill the Guardians Of The Galaxy, if she recognised them as key to stopping Thanos from getting his hands on the Infinity Stones (which would be devastating to the Skrull invasion).