Obviously Whedon couldn't have killed Iron Man or anything like that. The point I've been stressing is that the creative process is collaborative and that Whedon is a monumentally huge part of that process. Nolan was given more control than most (for Rises at least) but that's really neither here nor there. The initial point being contested was that Avengers wasn't really a Whedon film.
Furthermore, I defy anyone to actually write down this so called 'Marvel formula' that they force all directors to use that isn't so generic it could be applied to any and all big action blockbusters.
Nolan had the creative control in the whole trilogy. At least in most aspects.
In The Avengers, those characters were already established. It wasn´t Whedon´s job to decide how Captain America was going to look and act on screen, or who was gonna play him, because those decisions had already been made. The foundation had already been established. He didn´t have to decide how that Universe was going to look and feel, because that had already been decided. All those characters had already been played with, so he had to stay true to the blue print. He couldn´t just decide "oh, hell, i don´t like this character acting like this, so in this movie he is going to act completely differently".
As for the Marvel formula:
- The story is very action-driven and the plot is pretty simplistic, for the most part. Very few layers and very straight to the point. Most Marvel movies are very easy for a 9 year old kid to follow and understand.
- Colorful, happy, family friendly, for the most part. Tons of eye candy also.
- The dramatic moments are presented in a very soft way and are quickly discarded in favour of more happy and funny moments. There´s a lot of tragedy in these movies, but they don´t feel tragic. TDK feels tragic. I can´t say the same for The Avengers.
- Tons of attempts at humour. The characters are constantly trying to act funny. Lots of cheesy one-liners and "casual" moments, to make the heroes feel more relatable.
- Very few risks taken. The plot is generally very safe and predictable, not only in the way it treats its characters, but also in the way the story is told. You look at Rises, for example, that´s not a very conventional way to tell a super hero story. We don´t get much Batman, and we don´t see him until 45 minutes into the film. This is not safe or conventional, because it´s not what people are used to. This is actually pretty risky and turned a lot of people off, especially kids.
This is the Marvel formula.