Here is how I would do the movie,
It starts in the past, its a period film. the 70s, or around that time. It would also have a Steranko Agent of SHIELD psychedelic pop art vibe to the film.
A young Nick J. Fury a soldier, youngest of three, who grew up in Hell's Kitchen. (He did and it would connect it to the Netflix films.) When he is done with a tour in Vietnam he is disillusioned. As he applies for work and tries places like the CIA events unfold that get him recruited by SHIELD. Where he is trained first hand by one of the top agents, maybe even director at the time, one of Cap's original Howling Commandos, Dum Dum Dugan (he would be about 75 though so maybe they would have to fudge the numbers a little.) Dugan is like a grizzled curmudgeon of a C.O. But he is actually a great guy and lovable. Sort of like Killowog in GL comics.
Nick Fury is a field agent, going on missions. One such mission costs him his eye. We also see eventually that his black hair gets gray on the sides like in the comics.
His missions take him up against the remnants of Hydra, and along the way he meets his Catwoman type love interest and competition of sorts Valentina Allegra de la Fontaine. They are both new agents and training.
The film needs a big bad Winter Soldier tangled intrigue type problem for them to face. And the characters need an arc, maybe Fury starts out disillusioned and wondering whats the point and in the end sees the point and why what he is doing is so important.
The film would help fill in some of the blanks and bridge some of the gaps between the events of Captain America #1, and Iron Man #1. We get to see Fury in action and see him become America's best agent and most dangerous non-powered human being. And watch him get started on the path that eventually leads him to be the man he is in Winter Soldier. And we could even get a glimps of sorts of a young Hank Pym/Ant Man in action.