That would definitley be an interesting route but I don't think they'll get the rights back from Fox in time for the Skrull. Also I don't think they'd want to have another alien invasion if Whedon wants to keep it more personal.
I think Masters of Evil would be a great way to show an updated radical version of HYDRA with Zemo at the top trying to carry on for the Red Skull. Have him send in someone like the Ghost to steal Iron Tech and the Phase Two weaponry and break out the Abomination to create a response team to the Avengers as well as some new HYDRA foot soldiers and Rocketmen. So you'd have big guns like Zemo, Abomination, Crimson Dynamo, Ghost and maybe Amora and Skurge (though I don't know if they'd want another Asgardian villain after Loki) to fight the Avengers while HYDRA and Rocketmen attack Washington DC (since you wouldn't want to do New York again). Very Liberators-esque but without the heavy-handed attempts at politics that Millar had.
It may be too much but I think Stark and SHIELD finding out their weapons have been stolen as well as an almost copycat version of the Avengers would cause as much distrust and internal strife in the team as much as a Skrull invasion would.
I just hope they don't do Civil War.