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At the end of Iron Man 2 there is a map on a computer screen with various blips indicating different characters from the Marvel Universe. This is the kind of blink and you'll miss it Easter Egg that also says, “Don't worry guys, we've got this.” Given Joss' role with Marvel, he knows about all the secrets in the upcoming films, so is it too much to ask that we get hints at the upcoming movies?
Marvel has foreshadowed throughout the films they've made. Iron Man, of course, had the inital "Avenger initiative" conversation. The Incredible Hulk had the frozen Captain America briefly appearing in an alternate opening, and Tony somehow had Captain America's shield in Iron Man 2. These aren't the kind of things they decide on the day of, so we should be expecting more teases like that.
The show won't air until after Iron Man 3 has been released and around the same time that we'll see Thor: The Dark World. This is good timing for two reasons: they can hint at what might be going on in Thor: The Dark World without outright spilling the beans, and they can lay the groundwork for Captain America: The Winter Soldier. Marvel Studios has done a phenomenal job of making their films stand alone and connected at the same time. You don't have to see every movie to appreciate the one you're watching, but if you've seen them all then there are pieces inside to connect the dots and they shouldn't treat S.H.I.E.L.D. any different.