That is a bit of an exaggeration though. You had one film about the Cosmic Cube, and one film with Loki BEFORE The Avengers, which is designed as a cross-over vehicle. All of the films stand on their own pretty well. You did not need to see Iron Man or Thor to enjoy Captain America. I think we've seen the last of the Cosmic Cube, and possibly Loki, unless he appears in Thor's sequel. You can't say that The Avengers and the films leading up to it were about Thanos; he appeared for a few seconds. I'll bet the next round of films does what this round did; introduces the antagonist (Thanos) and Macguffin that will appear in the crossover film.
I'll be honest that I have my doubts that they can pull it off as effectively again.
I'll be we do see hints of the Pym/Ultron/Wonderman storyline. I would be VERY surprised to see Tony battle the bottle.
I think the movies distill the comic-reading experience and blend it with mass-market sensibilities. If you want a video version of the comics, then watch the animated Avengers: Earth's Mightiest Heroes, it is really good.
I want filmmakers to adapt the rich history of Marvel for film; I don't want them to follow it with some insane level of detail. I am not one of the people that cared that Spidey had organic webshooters in the Raimi films. They retained enough of the essence of the character to satisfy me. The only thing this change meant for Spidey was that Raimi never had to show him changing cartridges or explain how it works.