Six interconnected superhero films formed what is officially dubbed "Phase One" of the Marvel cinematic universe with The Avengers serving as the closing chapter. It wasn't until last summer however, with Captain America: The First Avenger and Thor did moviegoers get introduced to the larger cosmic universe and the otherworldly characters it hosts.
The Tesseract, or the Cosmic Cube as it's more commonly referred to as, became the McGuffin that drove the plot of The Avengers, forcing together the characters we met over the last few years and throwing them headfirst into a battle against Loki and his army of alien invaders. Loki was introduced in Thor and after putting on a show this summer, returns for his brother's sequel Thor: The Dark World next fall. But as we learned during a few off-planet scenes in The Avengers, Loki was merely a servant of someone and something much greater.
When Joss Whedon was brought in to helm The Avengers he completely rewrote the script previously drafted by Zak Penn. Marvel President of Production Kevin Feige only had a few guidelines for what Whedon's film must include: a Tesseract-powered portal opening in New York leading to an alien invasion. The Chitauri and their leader who showed up during the mid-credits sequence, Thanos, were selected by Whedon, and it was done so very intentionally.
For years, Feige has namedropped the Guardians of the Galaxy as a property he and Marvel Studios were legitimately interested in adapting into a feature film in an effort to bring fans deeper into the cosmic side of Marvel Comics. If Iron Man were a B-List character before he got his own movie, the Guardians are D-List. The success and acceptance of The Avengers and its sci-fi elements has allowed them to take even greater risks and as we learned (officially) at Comic-Con, that's exactly the plan. It's always been a near certainty that Thanos would return for Guardians of the Galaxy but his role in the bigger picture plans for the future of the franchise hasn't been so clear.
On the Screen Rant Underground podcast we talked in detail on several occasions about our theories of Guardians introducing a new set of characters to battle Thanos in a story that would serve as a lead-in to The Avengers 2 the following summer. Since that time, Joss Whedon signed to write and direct The Avengers 2 with a release date in May 2015, meaning it's picking up where Guardians of the Galaxy will end. Can we then expect Thanos to be the primary villain of The Avengers 2? Yes.