This isn't surprising. Whedon is, first and foremost, a writer, with Serenity being his sole feature directorial credit. In addition to creating and running Buffy the Vampire Slayer, Angel and Firefly, he wrote (and often directed) many of the strongest episodes in both series. His feature writing resume isn't quite as stunning, filled with box office disappointments like Titan A.E. and outright bad films like Alien Resurrection, but as a shameless Whedonite, I'll chalk that up to other directors not knowing how to handle "his style."
Speaking of this style, if he is indeed rewriting The Avengers and Captain America, how much of Whedon will we see in them? Whedon has a unique style and he loves clever banter and amusing wordplay (although one man's witty is another man's precious, hence the Whedon naysayers). Will Whedon tone himself down for consistency's sake? Or will he go all out make these script's his own? Knowing that Whedon is a true comic book geek who loves these characters, I think he'll find the proper balance between the two, making a product that is unmistakably his own while staying true to the Marvel universe.