Most notably, he shot an entirely different ending that wasn't used (and if a story that has "different ending" in the headline wasn't a spoiler warning enough, that's your problem).
The alternate ending (which will be included on the Blu Ray) featured Quicksilver waking up from his bullet wounds and standing next to Scarlet Witch in a new costume. Whedon stated that he shot the ending with Quicksilver as a New Avenger because he wasn't sure if Marvel was going to let him kill off the character or not, and Marvel might have been interested in using him in more movies.
Obviously, it turns out they weren't worried about that at all.
You can listen to the entire podcast here:
Other reveals from his interview as pointed out by Cosmic Book News.
- It was Whedon's idea to have The Vision pick up Thor's hammer, but he only brought it up as a joke.
- He wanted Captain Marvel and Spider Man in the movie.
- Grey Hulk was supposed to fight the Hulkbuster armor.
- Whedon wanted to have Bruce Banner look up at the stars and ask "Where in the world am I not a threat?", which would have alluded to Hulk leaving Earth.
- Loki was supposed to be in the Thor dream cave sequence, but Marvel couldn't get Tom Hiddleston, so they got Idris Elba for the scene instead.