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#6 'ONE SHOT'/STANDALONE EPISODES
I'm talking in comics parlance here, and I realize Marvel has already used the term for the short films on the Blu-rays, but the one shots and standalone issues are a long-standing tradition in comic books as a break between the ongoing storylines that we normally see.
While it seems Marvel's S.H.I.E.L.D. will be a pretty serialized show, I'd like to see some episodes that focus singularly on one character or one event specifically, but where S.H.I.E.L.D. can differentiate itself from other TV shows that do this is by bringing in the actors from the films. An episode that is about Nick Fury, Black Widow, or Hawkeye would be huge for the fans and a great storytelling opportunity. They could even go the direction of telling the story of the fabled “Budapest” mission that's mentioned in The Avengers.
Another way that Marvel could shake things is up with the one shot formula is to try some more experimental things (likelihood: 5%), because Joss has a history of doing that with his previous shows. I'm not saying they should do a musical episode like Buffy, but there was one episode (“Hush”) that carries an aesthetic seen in some one shots: no dialogue. Trying out different things to make your show more interesting and a reflection of the source material is a good idea that Marvel should consider, but might shy away from due to potential harm to the brand.
Marvel could also go the traditional route of the one shot and have episodes focus on heroes they want to develop into shows. Normally when a one issue one shot comes out, it's to test the waters for that character's future and I can see the same thing being done on this show for future Marvel shows. Daredevil, Heroes for Hire, and The Punisher are some examples I want to see them try out.