A lot of people presumed that the alien race in The Avengers were the Skrulls; this was reasonable for various reasons. Number one, it would mean that Loki teamed up with Super Skrull and that gives way for the whole cosmic universe film saga that Marvel is planning. Then Kevin Feige said that the aliens were not Skrulls, I repeat not Skrulls. Now Joss Whedon has stated that they are the Chitauri. Now Chitauri are an alien race that exists only in the Marvel Ultimate Universe and upon encountering the F4, they reveal themselves to be known by many names including Skrull. Chitauri are Skrulls and in the Ultimate Universe they do have a ... form ... of shapeshifting and hence you lied Kevin, the Skrulls are in The Avengers, but they are called Chitauri.
Now, my take on a Justice League movie would be similar to the Avengers. But first, have the Superman and Green Lantern series build up two things, Earth and Space. Man of Steel 1 and 2 give the basis for what Earth is in this universe and Green Lantern 2 shows what happens in Space. Then have the Batman reboot and the Aquaman film be interconnected with each other and dovetail right into the Justice League movie which introduces Wonder Woman.
In my story for a Justice League movie, the alien race called the Tsaurons arrive on Earth, led by General Ortiir. They hide amongst humans for a while, but ally with wealthy businessman, secretly assassin, Slade Wilson to infiltrate the goals of the Earth. They unleash the Braniac virus on the Earth and the heroes unite to save it, but discover that the Tsuarons plans include far more than to just conquer Earth. What is the Tsaurons home planet? You guessed it, Apokolips! That paves the way for Man of Steel 3!