I think it is a good move, theGA will feel like they have seen everything Marvel has to offer in The Avengers, and then a flick like this could surprise them.
I see what you're getting at....but they will not be showing us everything SHIELD has to offer in the superhero movies.
What the *new* pull could be...ok, we have seen superheroes vs supervillans, but what do normal government agents do up against super-villans?
Agents flying about the city on sky-sleds fighting super-villan/s, stuff like that. Agents using tech against powers, sometimes it's more interesting to see how non-powered folk go up against superpowers. and by the Avengers we will have seen the most powerful in action, so let's see some inventive ideas showing agents vs suppowers.
Because they should have superpowered villans in there, to distinguish it from other secret agent movies like Bond/MI/GI Joe.