... specifically, over at DC, during its Millennium crossover?
Think about it:
Due to ancient beliefs of an alien culture, they've decided to finally act in order to accomplish their long stated goals. (The Manhunters wanted to stop the Guardians from helping the next immortal race to ascend on Earth, while the Skrulls apparently have some deeply held religious philosophy to dominate the Earth.)
In doing so, they've either replaced existing heroes or supporting cast members, or used cover identities to get close to the levers of power and our heroes. (Here, we apparently have Skrulls as high-ups in government, the Initiative, and at least 1 in every title. Millennium had a Manhunter infiltrator in every title across the line for that crossover, including such luminaries as Lana Lang and commissioner Gordon.)
I think now we know why Marvel didn't get too annoyed at DC borrowing the premise to their Prime Sentinels in their big crossover a few years back.
The main plot of Secret Invasion essentially follows a very archetypal kind of story, which we've seen many times before, with numerous variations. Essentially it's the 'Invasion of the Body Snatchers' type, "Our group/institution/society has been infiltrated by enemy invaders and we can't tell them apart from us!!!" thing.