We know that the mystery aliens are not the Kree or the Skrulls. Joss has made that pretty clear. I think they are the deviants. And as we all know Thanos is an Eternal with the Deviant gene.
Maybe they will use the Eternals to explain the god-like power of the Asgardians or Olympians or even Atlantis & the Inhumans...
If the Inhumans are introduced at a later date it could be an opportunity to introduce Wanda & Pietro (yeah I know they're not Inhumans) but if Marvel can't use mutants I would be prepared to accept them as Inhumans if we get them in the Avengers!!!
Regarding the Avengers if we are getting Loki & aliens in the first movie then you have to have something different in the sequel. I would hope for something like Hydra/AIM, with MODOK or a returning Red Skull & maybe even Ultron! If Thanos is teased in the first movie I would expect them to do the Infinity Gauntlet at some point, maybe in Avengers 3. Unfortunately this leaves us without Kree/Skrulls & no Captain Mar-vell or Ms.Marvel :o(
Mind you as the Kree were supposed to have created the Inhumans maybe Captain Mar-vell could be introduced that way. Maybe as a Kree ambassador for our solar system.
So...
Avengers Assemble - 2012
Loki forms an alliance with the Deviants who were driven from earth long ago by the Eternals. Loki promising them a return to earth, uses them and betrays them after he is defeated by the Avengers. Thanos (leader of the Deviant army) swears his revenge.
Mighty Avengers - 2015
The Red Skull returns to lead AIM with MODOK. AIM scientist Simon Williams sabotages Dr.Pyms new Ultron defense project for SHIELD. Ultron takes over the world computer network & threatens nuclear apocalypse using the Godseye satellite (Hulk is lost in space destroying it leading to a Planet Hulk movie...) Ultron & AIM also create the Vision & Wonderman to fight the Avengers but obviously they switch sides and Wonderman sacrifices himself for the cause. Ant-man also redeems himself after deactivating Ultron from the inside.
Earths Mightiest Heroes - 2018
Thanos returns with the ultimate power, the Infinity Gauntlet! The heroes of Earth must join forces with those of Asgard, Olympus, Attilan & Atlantis to stop him.