After he is uncompromised, he asks her how she's handling it, mentioning they aren't trained to handle monsters and magic. She's a spy.

Both of them would shine more in a Shield/Nick Fury movie where espionage and assassination/more mundane battle are the focus.

I could very much see a movie where the shadowy council seizes control of SHIELD from Fury, angry over how he first ignored their order and then informed Iron Man. Even though it worked out, it wasn't what they ordered. Then you have Fury, Widow, Hawkeye, and Cobie Smulders' character dealing with the council and other enemies. Throw in a couple hints at bigger things, too. (Maybe the council brings in someone like Pym against his will, that kind of thing. Or they could do the thing I mention below in my Coulson post.)

Even Captain America is very limited by his inability to fly/jump up buildings. You'll note that he frequently is using a gun himself in his movie and Avengers. He can take more hits and do more damage with a punch, and also throw his shield, but otherwise he's just a soldier in a battle among superheroes.