I've always felt that the Marvel Cinematic Universe takes its cues more from the Ultimate universe than the main comic universe. In which case, what about
Captain Carol Danvers a.k.a. Miss Marvel as the boss character? In the Ultimate-verse, Danvers is a regular human and SHIELD operative who held the director position after Fury. Plus, it would be fitting that Miss
Marvel headlined Marvel's first real foray into TV-land.
Also, instead of an ALIAS-esque story that everyone seems to be going for, here's my pitch for a SHIELD series:
It takes place shortly after the events of The Avengers. New York is still a mess, in the midst of reconstruction, and superpowered nutjobs are on the loose trying to take advantage of the chaos to carve themselves a little piece of NYC. The police are outmatched and the army can't intervene on home ground short of a full-scale war. Homeland Security's response? Deploying the Strategic Homeland Intervention, Enforcement and Logistics Division a.k.a. SHIELD. The New York task force is led by Agent Carol Danvers. Enver Gjokaj's character also returns as a police officer who is acting as a liaison between the police and SHIELD.
The first season will focus on the recovery of New York following the Chitauri invasion. Director Danvers is tasked with restoring order with regards to superhuman threats. She feels their activities are a little too organised and conveniently timed, instead wondering if there is a connection between them and Loki's allies from the Helicarrier attack. Meaning, along with the monster-of-the-week setup, there are some investigative/espionage bits thrown in as well.
Along with all the classic superhero stuff, the show could also touch on the human aspects following a major disaster. At first, the people are happy and thankful for SHIELD's (I mean, 'Homeland Security') presence. But as weeks stretch to months and over a year with the superhuman threats still ongoing, civil unrest develops. Especially when they find out of the advanced weapons that SHIELD developed from the Tesseract that could potentially solve the problem overnight if distributed to the civilian population.
In the season one finale, Danvers is critically injured after getting hit by a car during a battle with the season's Big Bad. Her replacement, Marvin Flumm (Danver's actual replacement in the Ultimate-verse but also the name of a supervillain in the main universe) is much more shortsighted and doesn't/refuses to see the link between the New York supervillains and SHIELD's enemies. Needless to say, he doesn't mesh well with the team who are still loyal to Danvers. In the end, Flumm (or someone else, with Flumm as a red herring) is found to be a mole and this discovery forms the first link between the supervillains and HYDRA.
Also, Danvers at some point recovers from her injuries and in addition, briefly gains super powers (taking on the alter ego identity of Miss Marvel?) but this is in the end stolen by a certain unidentified individual with the ability to steal other people's powers (essentially, a lawyer-friendly version of Rogue).