Several pieces of cut footage have recently been released, including an alternative opening scene, and Whedon explained the reasoning behind some of the cuts in an interview with Vulture.
Of the alternative opening, which centres on Maria Hill (Cobie Smulders), Whedon said that there were "two factors" informing its omission from the theatrical cut.
"One: the movie was three hours long. Two: audiences didn't respond to it as well in the movie as I think they would as a DVD extra. Most of them didn't know who this character was or what the context was, and they were like, 'Uhhh, I don't know why I'm supposed to be personally involved in this character I don't know'.
"The rollout to the Avengers getting to Loki was so gradual that people were getting restless. I thought Cobie nailed it, and the reason I thought it was necessary is because I was trying to make a war movie and I wanted to give context that something bad had happened in the past."
"In a war movie, you don't know who's going to live or die," Whedon went on, "but you do know that this war happened and that [the characters] are going to be in a dire circumstance, and I wanted to create that atmosphere. I was able to get what I needed without doing that. It was tough. I hated cutting it."
Whedon will return to write and direct The Avengers 2.
The UK DVD and Blu-ray releases will reportedly not include commentary from Whedon, because the track was not completed in time.
Watch the alternative opening scene for The Avengers below: