Well the references weren't made simply as nods. Come on, it has been their business startegy for sometime now. That is more than obvious. It's the primary reason these four characters rights were acquired.
In some movies, namely Iron Man 2, and to a smaller extent Thor, the addittion of "SHIELD" and the "Avengers Agenda" goes out of its way and derails the main focus of the movie at the expense of the title character.
Pretty sure the studio even meddled so much in Iron Man 2, that it is one of the reasons Faverau bounced from future projects. Hell, you can tell when his film gets disjointed with the studio's agenda. The first 30 mins feel like a legit sequel to the first film, and is right there with the original Iron Man. Then we get the scene of Stark in a donut shop, being riddled with questions from Sam Jackson in all black with an eye patch, and the completely useless character to the narrative Scarlett Johanson's "Black Widow" at his side.
I understand how my opinion won't be popular. But it is my opinion, and I just wanted to share what I consider constructive criticism. All the MCU films have been to me very average, apart from the original Iron Man.
Some down right bad, but are disguised and glossed over by fans of the character merely because minute details correlate to their comic book counter part, or the look of the characters and films are ultra faithful, or production value is good.