I'd just like to point out that it's a bit unfair to characterize the degree to which SHIELD normally interacts with superheros by showing how often they show up in superhero films. Um... Because they're superhero films. So there's going to be superheros in them. Doesn't tell us what percentage of the SHIELD mission mandate actually involves working with superheros though. It's quite possible that 99% of their time and resources are used dealing with other stuff, and 1% interacting with superheros. But since all the films so far have revolved around superheros we tend to see SHIELD involved.
Maybe the whole point of so little involvement was to make make it more clear that this isn't really what SHIELD focuses on. Saying "that's strange because they were always involved in the other superhero films" doesn't work if their intent is to suggest that that was the exception and not the rule all along. You just happened to see films that included the half dozen or so times they were directly involved with superheros.
Or something like that. Dunno.