Actually, the films and TV shows do not coordinate with each other. The films ignore the shows altogether. For example, there was a sub-plot in season 2 of AoS in which Coulson is getting the helicarrier ready for its appearance in Age of Ultron. But Joss Whedon killed Coulson so as far as he is concerned the helicarrier in Ultron is just a gift from "some old friends" even though it means ignoring the TV show Whedon is an executive producer on.
Some of us were just having a lengthy conversation on this subject in the
AoS Season 3 thread recently. The film was in production
before season 2 of the show, and the sub-plot you mention was devised to tie in with the film. However, the film
did subtly and obliquely acknowledge the show by having Fury mention that he's "not the Director of anybody anymore," having appointed Coulson to that position at the conclusion of Season 1.
The Netflix shows are even worse. They for some reason aren't allowed to make direct references so instead we get characters talking about the green guy or the guy in the iron suit. There's a million skyline shots of NYC and no Stark/Avengers tower in the background. They pack in as many subtle references as they can (like Roxxon which has been around since the first Iron Man IIRC) but the idea that it's all connected is still bound up in legal claptrap none of us really care about. As a result we end up with a lumpy continuity in which the shows take place in the movie universe (in as much as they are allowed to, see above) but the movies pretend the shows don't exist.
I am not aware of any prohibition on making direct references in the Netflix shows. I think they choose to do that because it seems more natural and conversational than having people always refer to "the Hulk" or "Iron Man" or "Thor" by those names. They
have directly mentioned the events of the Battle of NY several times, and it is actually an integral part of the basic premise of Hell's Kitchen being less cushy and gentrified than it actually is today in real life. The lack of the tower is simply due to budgetary reasons, and is really nothing compared to the relatively common practice in TV and films of often having
entirely different cities stand in for the locations in which they are intended to be set. I agree that it would be nice if the tower were there, sure, but it's nevertheless a minor point that is only a big deal to people who obsessively strive to maintain an "in-universe" perspective on that level of detail instead of remembering it's all just fictional entertainment.
That helicarrier in Age of Ultron should have been staffed by Coulson and his crew. Daredevil and Jessica Jones should be able to see the Avengers tower as they're prowling rooftops in Hell's Kitchen. Et cetera. But they don't coordinate and those of us who are watching closely might not know exactly what is wrong with the picture except that there is something missing. I wish the movies and TV shows would acknowledge each other more formally and in a more meaningful manner. To paraphrase a poster here no one will be confused by references to Marvel products in their Marvel products. But the TV and movie divisions have split and are further apart now than they have ever been.
If the hellicarrier had been staffed by Coulon & Co. this would have actually
contradicted the TV show's continuity, because Coulson there decided to maintain the illusion of his death and work behind the scenes in the shadows. He didn't want the Avengers or even his girlfriend to know. But the real issue is that it would
absolutely have confused the general moviegoing public that doesn't watch or care about the shows. The reality is that the franchise is driven overall by the films and the shows are merely ancillary spin-offs, and that's why the shows promote and mention the movies and not vice versa. Another practical facet to this arrangement is that films are in development and production for
years, whereas TV shows are made on a much shorter timescale. Multiple seasons of multiple shows might come out in the time one movie is being written and filmed. So even if it made any sense dramatically or financially (which it doesn't) it would be logistically impossible for the films to play catch-up to the shows instead of the other way around. The two divisions
do coordinate to the extent that the film division makes its plans for the movies known to the TV division so that they can write around them in the meantime (as
AoS did with the hellicarrier sub-plot).
