In that script, the villians are Loki and the Skrulls. Basically, Loki tips the Skrulls off to the fact that the cosmic cube is on earth and they want it to restore their home world, or take over Earth, etc. It turns out that Maria Hill is the Skrull Queen in disguise (nice nod to Secret Invasion) and the final battle is Thor vs Loki in the sky, Iron Man and Fury vs Skrull Queen on the Heli-carrier and Cap and the rest vs the Skrulls on the ground. I also read that the Hulk does fight the Avengers, but it is a short battle, probably when they meet him. Also I read that Cap fights some SHIELD agents, which is probably right before the Times Square scene with Fury (i.e. post thaw).