I am pretty sure that Joss Whedon won't direct The Avengers 3. I've heard rumblings from behind-the-scenes that he's pretty much finished with the Marvel stuff, plus doing two enormous movies like that in a limited time span is exhausting. On top of that, no director has ever worked with Marvel more than twice, and the only person who has done that was Jon Favreau, the first guy on board.
So if he leaves after The Avengers: Age of Ultron, who steps into Joss' seat for the third film? After seeing Guardians of the Galaxy and how effortlessly it combined humor and emotion and excellent large-scale action, all while balancing many characters, I thought James Gunn would make a good replacement.