That way the storyline can remain mostly separate from whatever HYDRA arc unfolds in Age of Ultron or Cap 3.
Though presumably the people working on Agents Of Shield have full access to all the currently planned out plots for AOU and Cap 3.
The MCU is pretty clearly a case of the right hand knowing what the left hand is doing.
Of course, but as I've been pointing out all day, it's not about what the creators know, it's about what the audience is expected to know. The whole reason to do works in different media is to draw in different audiences. It is a given that not everyone who sees the movies will watch the show, therefore, anything that happens in the movies needs to be independent of the show. Also the moviemakers need the freedom to do what they want without being hemmed in by the show -- while conversely, as others have pointed out today, the show needs to be able to develop its own storylines that aren't purely dependent on the movies.
More basically, even with the close supervision and coordination they have, the movies and the show are from different creative teams operating on different schedules, and that makes close coordination difficult. It's simply more convenient for both sets of creators if they're able to tell their own mostly independent stories with only occasional overlap.
Heck, look at any two Marvel comic book series and you'll see that they do much the same thing, striking largely independent courses with only occasional convergence and cross-reference. Even two series about the same hero at the same time, e.g. J. Michael Straczynski's
Amazing Spider-Man and Paul Jenkins's
Spectacular Spider-Man, generally run in parallel with each doing its own independent storylines, overlapping minimally. There was a ton of stuff Jenkins was doing in
Spectacular that Straczynski never even mentioned in
Amazing, even though these stories were all supposedly happening to the same people at the same time.