So it's somewhat been confirmed that Guardians of The Galaxy will be the lead in for Avengers 2. Cosmic villain Thanos was teased at the end of Avengers and the Guardians have links to the Mad Titan sort of a lock that he'll be the baddie for that film first. Eventually, having Thanos and Mistress Death the main villains for Avengers 2. Fans had been upset that the less popular Chitauri were chosen over the Skrulls as Loki's army (thanks to Thanos pulling the strings). It's likely that Thanos could end up using the more dangerous Skrulls to conquer Earth if he needs a stronger force. Also, two possible additions to the Avengers lineup have links to the Skrulls.
The Mad Titan is planning on creating his own empire by conquering the universe. To do this he's going to need his own army which likely will see the Chitauri being replaced with a stronger group. Considering how easily they were defeated by the Avengers. Thanos has used the Skrulls for his own means in the past fuelling the Kree and Skrull war on Earth. It wouldn't be hard to imagine him using the shape-shifting Skrulls to obtain the infinity gems in Guardians and then have them infiltrate the Avengers and SHIELD to prepare his invasion of Earth and Asgard (for the infinity gauntlet/cosmic cube). Joss has been talking covertly about a smaller sequel. Perhaps he could end up making it more like a thriller ala Ten Little Indians/The Thing which could be interesting. Having the Skrull force in smaller numbers than the overboard amount of Chitauri in the first film.
The Skrulls main threats is their advanced technology which enables them to reproduce superpowers and abilities. This could be a very dangerous combo if they're able to make a group of super soldiers, iron men and godlike goliaths. Throw in the fact they can make themselves look like anyone at anytime and you've got a much superior force compared to the Chitauri. Not to mention a good way to lead into the war with the Kree or introducing them (along with Captain Marvel/Ms. Marvel) to begin with if they're not already mentioned in Guardians. This could also be a great way to have at the very least cameos from Wolverine and Spider-Man in the sequel.
Having the Skrulls could also be a way to introduce audiences to Black Panther and Wakanda. Panther fans and Marvel fans alike were shocked Panther wasn't added to the Phase Two lineup. T'Challa was rumored for an introduction in Captain America: The Winter Soldier but nothing has been confirmed. However, if the Skrulls end up in Avengers 2 they could show up in Wakanda first to steal their advanced technology and vibranium for their own means. Recently the Skrulls tried to go up against Black Panther and the Wakanda army, having their asses handed to them. It could be a great way to have Black Panther join the Avengers team.
Another possible addition could be Hydra spy turned SHIELD Agent/Avenger Jessica Drew (Spider-Woman) joining the group only to be found as being Veranke the leader of the Skrulls in disguise. It would be an obvious one but her inclusion would make a great complex female character with powers which the franchise is currently lacking. While it's likely the female lead (Anna Kendrick) in Captain America: The Winter Soldier is Sharon Carter, another possibility is Jessica. That could be a great setup if Steve's fellow soldier (love interest?) turns out to be the enemy the entire time.
