I'm not the least bit worried by Whedon's film resume. In fact, lack of experience works to his advantage.
As illogical as some may think it is, the fact remains that in the genre of superhero film, it is the (relative) noobs who make the best material, while film veterans still haven't grasped what makes the genre tick.
Before their respective superhero franchises took off, the film resumes of fan-favorite directors included mainly:
Tim Burton:
Beetlejuice; Pee Wee's Big Adventure
Chris Nolan:
Memento; Insomnia
Jon Favreau:
Made; Elf; Zathura
Bryan Singer:
The Usual Suspects; Apt Pupil
On the other hand, established directors with acclaimed careers have rarely been able to duplicate that same kind of success --- Joel Schumacher,
Kenneth Branagh, Joe Johnston, Ang Lee, Martin Campbell.
The formula is simple: find a relatively inexperienced film director from a genre *outside* of superheroes, and they'll usually be able to bring a fresh take on the subject matter to make it a hit. The formula doesn't always work --- it definitely didn't for Mark Steven Johnson or Tim Story or Louis Leterrier --- but for the most part, Marvel and DC have been able to find lightning in a bottle with the novices instead of the veterans.
So that places directors like Joss Whedon and Patty Jenkins
(Thor 2) squarely in the "safe bet" column.