If I'm going to convince the world that this movie sucks, the first thing I need to do is tackle is the most pervasive argument from its apologists, which is that the movie had an inordinate number of main characters and so even just putting this many characters in a movie is a triumph.
On the surface, this seems to make sense. After all, if the audience doesn't have a character they can identify with, it's hard to be invested in the movie. In fact, this is the truth with Avengers, but people tend to compare it to an idea in their head about how bad it could have been (perhaps because this line about "fitting in so many main characters" has been repeated so often.)
But, here's the thing, when you make a movie, there are no rules. Yes, you have four characters in this movie who starred in six of their own movies up until this point, that does not mean that they are all protagonists and that they should all get equal screentime. Not true, and not even a good idea, actually.
Let's say that the numbers of protagonists in this movie as it stands now is four: Cap, Iron Man, Hulk and Thor. Hawkeye is gone for most of the movie, Fury, Hill, Coulson and Black Widow are all just there to do there jobs. The other four guys have a motivation and need a motivation for being there. Breaking it down this way shows how strange it is to declare that the movie has "soooo many" main characters.
Tons of great movies have managed with four protagonists, but with one caveat: they focused the story on one. The Dark Knight has Bruce, Rachel, Harvey and Gordon, with Bruce at the forefront. X-Men had Wolverine, Cyclops, Jean Grey, Storm and Rogue, with Wolverine at the forefront. Star Wars had Luke, Leia, Han, and Lando, with Luke at the forefront. Lord of the Rings had...fucking, a billion people and arguably two main leads: Frodo and Aragorn. Casablanca, Seven Samurai, Saving Private Ryan, The Prestige...all of them had a lot of protagonists in them, and they all work. I would argue that in each of these movies, they were good enough at characterizing the "side-protagonists" in a short amount of time, but focused on one protagonist as their "main character".
So, let's dispense with this notion of there being "too many characters" in Avengers. The problems with the Avengers cast are that there is no focus on one character, and that the characters are not characterized well. (Or, in some cases, characterized in the opposite direction. I'll talk more about this later.)
But ok, I get that making a movie with four characters who were previously stars in their own solo movies might make things weird, but again, there is no rule that says we have to split the movie four ways. So, the question is: Who should the main character been? As the movie stands now, the audience doesn't "follow" any one person's arc throughout the movie; Following someone -- anyone -- would have been preferable to this. I'll give you four options, you think about what the movie would have looked like in each of them, and then ask yourself if you think that the way Whedon wrote his script and characters was better.
1) Iron Man - I have a few simple reasons for suggesting that Tony would have been a good character for the audience to follow throughout the movie. First, he's arguably the most popular character in this movies. He even got top billing. Second, Iron Man movies make the most money. It would have made good financial sense to do this. I'm not saying that decisions that make the most money are always good, but again, someone would have been better than everyone. Third, Whedon can write Tony's character well -- snarky, quippy, stuck-up and making up dumbshit words.
2) Captain America - I mention in the bias page that I like Steve Rogers the most out of all these characters, so bear that in mind, but, if the point of this movie was to "bring the Avengers together as a team" than perhaps the group's leader would be the best at that and should be the focus. In addition, in this universe, when we last left all the other characters, they were in limbo. Tony's being Tony, Banner is off missing somewhere, Thor is up in Asgard. Steve, on the other hand, has just come out of his coma and is open to a lot of characterization from that. It would have been a good place to start following him trying to get adjusted while trying to bring everyone together. (Compare to the current "getting together" strategy, which is "the government says so." Is this heroism? Does this make you root for our protagonists?)
3) A Minor Avenger - What I think people get confused about when discussing this "main character" thing is that they think that having four solo stars in the same movie is an obstacle. Really, it's a blessing. You have at least 90 minutes with each character already written; the audience knows who they are and your job as a writer is basically done (as long as you don't completely change what was written in the other movies). So, with so much room to play with, why not focus the story on Hawkeye or Black Widow. Again, Whedon wrote most -- not all, but most -- of Black Widow's scenes well. I wouldn't have minded following her throughout the movie, since we've only gotten little hints at her character so far. Hawkeye even less so, since he's not even in this movie. This also adds a new element to it, in that both of these characters don't have "superpowers". They have to attempt to keep up with a god that shoots lightning by their skill alone. This adds tension, something that is painfully absent in this movie.
4) Fury, Coulson or Maria Hill - This is the most financially risky of all the choices, but storywise I think it could have worked. You have all these larger-than-life characters running around, instead of trying to get the audience into the mind of a billionaire or a green monster or World War II vet, just go with the everyman character. Seeing Coulson go up against Loki was cool to see, wasn't it? You knew that the poor little guy was outclassed by a ton, but you admired his courage. That one scene made Coulson one of the most popular characters from this movie. (No, Joss, not because he died, but because he was the only character to do something brave and not whine about it in the entire movie.) Also, if you must have the "government makes the heroes act heroic" plotline, these characters are the government. Fury's task of bringing this team together could be the backbone of this movie.
Now, I don't claim that this are all perfect ideas, but again, compare it to the movie as it is now. Who's the main character? Who's story is this? Nobody's, despite the fact that there are tons of options.