OR something that I admit could be a terrible idea but I think could work if executed extremely well: Carter could sorta be our main character in the Avengers. Kind of like Myers in Hellboy except...not lame. Instead of some boring newbie, we could get to know the inner-workings of S.H.I.E.L.D. and life on the Helicarrier through the just-another-day-at-the-office grind of one their top agents. Then we'd be sort of re-introduced to our Avenger's through her perspective (and it wouldn't be a favorable one, as these freaks are treading on her territory and being treated like rock stars by the higher-ups) - of course as soon as that happened the spotlight would rightfully shift to them, but from a storytelling standpoint she could serve as easy exposition. And despite being cynical toward the whole Avengers project, she could reluctantly become the 1st person in the present day that Cap forms a bond with, since the guy should initially be a bit of a mess after learning everyone he ever knew/loved is long dead and gone. But she'd have to be a kickass entertaining character for the audience to be cool with this, and I wouldn't want anything romantic happening between them in the 1st movie. You know, maybe she's a bit anti-authority and is currently in a bit of hot water with Fury/her commanders and is forced, as punishment, to acclimate Captain America to life in the present (which she would consider 'babysitting'). So they could develop a kind of snarky rapport and she wouldn't even really like him 'till the end or something.
I know, I know, flame away. I just think they don't have to wait 'till Cap 2 to make her a major character. She could be the most prominent member of SHIELD after Fury that we know. And SHIELD will likely be a huge part of the Avengers - like, probably the main "setting" - so I think it would be a little weird if the only main character we know from SHIELD is Fury himself.