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I'm a big fan of Joss Whedon's stuff. And like most writers he has running themes throughout his work. For Aaron Sorkin the term 'Sorkinisms' came into common use when describing the themes that run through his work. While no one wants to be thought of as predictable, I am going to point out some 'Whedonisms'

I'll be using Buffy, Angel and Firefly to demonstrate these themes - his films could be referenced, but it seemed best to to concentrate on his TV work (and I couldnt get into Dollhouse because of the revolving personalities of the main character)

HIS CHARACTER'S WILL NOT HAVE A HAPPY LONG TERM ROMANTIC RELATIONSHIP

His main characters will be strong, decisive in action, charismatic but either self destructive or oblivious when it comes to romantic relationships. I cant think of any character that got a happy ending romantically.

Buffy had serious relationships with Angel, Riley and Spike, but none ended well. Angel could never be with her because "one moment of bliss turns him evil", so he left. It was for the greater good, but ultimately a doomed romance.
Riley was a solid character who left because he realized that he would always be second to her mission - he was also jealous of the connection Buffy and Angel would always have - and that while Buffy loved him, she didnt love him enough.
Spike was interesting because of the development. Their relationship started from a situation of emotional confusion on both parts. Eventually Buffy reverted to her usual personality, her confusion gone, while Spike developed as a character - becoming a champion in his own right - but Buffy didnt love him and in the end he knew it.

Angel as already stated above, his relationship with Buffy was doomed. Darla killed herself to save her baby. And Cordelia ascended before their relationship actually started. Then she got taken over by the big bad for season 4 and died.

Mal Reynolds relationship with Inara was always rocky, but as Firefly only ran for one season it was never really resolved

This theme is extended to the supporting cast as well. In Buffy Tara was shot. Xander left Anya at the altar, Oz left Willow because of "werewolf issues" and Cordelia left Xander because he had feelings for Willow.
In Angel we had the revolving door of Fred, Gunn and Wesley for a while (Fred and Gunn split because of trust issues and a murder, Wesley and Fred split when she died and she became Illyria. Doyle and Cordelia got one kiss before he died.
Firefly never had the chance to develop these aspects, however there was some tension between Wash and Zoe because of her relationship with Mal that might have been the seed of something more

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
Any relationship will ultimately fail

THERE WILL BE BANTER AND POP CULTURE REFERENCES

This is one of Whedons strongest character points, he uses an easy discourse between characters to show the audience how connected they are. It is also a quick way to show group dynamics for a series.
However he also uses banter during fight scenes to hide any negative emotions his protagonist's might show...for a while at least. This might be called 'smack talk' but its also a device for editing during a scene.
Characters also develop their own references - a vampire becoming "all fangy" for example

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
There will be lots of quotable stuff going on


THERE WILL BE ONE OR MORE TECH PERSON INVOLVED AND THEY WILL INITIALLY BE SOCIALLY AWKWARD

Buffy had Willow, Angel had Fred and Firefly had Kaylee - the techie seems like a constant character. Obviously S.H.I.E.L.D. will have tech people in the cast. Each character seems to blossom from a socially awkward genius to a fan favorite and secondary crush for the viewers. The tech character always develops most.

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
The techies will become invaluable to the series


FAMILY ISSUES

A characters actual family dynamic will be mostly strained or there will be absent parental figures. This is used for several reasons, the main one being group dynamic. Characters become more of a family to each other, so any sacrifice has more impact on them and us.
A paternal figure normally emerges within the cast - Buffy has Giles, Firefly has Sheperd with Angel being an exception because the actors are all roughly the same age (Angel himself acts as a father figure at times though). The paternal figure also develops some skills which make them an asset to the team (good in a fight)
A significant maternal figure has yet to emerge in Whedonisms - Buffy's mother had significantly less airtime than Giles

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
Judging by the cast, Coulson will be a father figure to the team


BEING GAY IS NOT THAT BIG A DEAL....
Gay characters are treated as totally normal people...which they should be. As a heterosexual male who has gay relatives, it surprises me at times that there is so much fuss made when a character is gay. Personally i only care that the characters are interesting.
Buffy had Willow and Tara, Inara was bisexual in Firefly and there were hints at a homosexual experience between Spike and Angel.
The thing is, any sexuality didnt really impact a character at their core- Whedon just seems to think that relationships are plot devices, it doesnt matter what type of romantic relationship a character is in, its doomed anyway.

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
A gay character


DEATH

Some characters will die...fact. Mostly its minor characters, but in series finales a core character (not the main character) can die.
But Whedon generally gets the audience to connect to a character before they are killed, so that the death has some meaning or impact and there is usually a reason.
In Buffy, Angel was killed to save the world. But his death also affected Buffy's interactions with Family and friends. Her mothers death affected her everyday life - had to look after Dawn and get a job. Minor characters such as Jonathan died as part of the big bads plan, while Tara's death turned Willow evil.
In Angel, Doyles death affected Angel's attitude toward his companions for a while, but also affected Cordelia by giving her visions (which tied into the arc which ran until season 4's big bad). Darla died so Connor could live. Lilah's death had an effect on the group dynamic and Wesley in particular.
Firefly had no exceptional deaths as it only ran for 1 season - i'm not counting the death in Serenity as i am not covering films.

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
A secondary character may die later in the season (more likely in season 2 if its a success)

CHARACTER TURNS

Several characters have switched allegiances during Whedons various TV series, even main characters have gotten close to being bad.
In Buffy the notable turns are Angel having the gypsy curse which turned him into Angelus. Willow became an evil witch for a while. Faith turned evil, Cordelia evolved into a scoobie associate instead of a vapid socialite and Spike became a champion with a soul.
In Angel Wesley turned on Angel and stole Connor, Fred tried to get murderous revenge on a teacher and was turned into Illyria in the final season, Darla, Lindsey and Connor all flip flopped at one time or another, Cordelia was a baddie and Angel himself got very close to being a baddie when he lost his faith in his companions and felt his actions against Wolfram and Hart weren't effective enough. And he turned into Angelus for a time.
In Firefly, Jane flip flops for a while during certain episodes.

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
Superhuman baddies may become allies or betrayal from within

AN AVERAGE PERSON WILL BE THE GROUPS MORAL COMPASS AT TIMES
In every series there seems to be a character who just seems average, but at points they turn out to be an essential moral compass for other characters.
In Buffy, Xander is just an average, unexceptional guy who managed to stop Willow from destroying the world by talking to her.
In Angel the role gets fuzzy, ultimately Lorne fills this role
In Firefly the role was Sheperd's

POSSIBLE IMPLICATIONS IN S.H.I.E.L.D.=
The main character will occasionally seek moral direction from another character


WHAT DOES THIS ALL REALLY MEAN

There may be some if not all of these themes present in S.H.I.E.L.D. or there may not....we'll have to watch to find out