Whedon said in an interview that this was done so that people who saw Avengers I but have not watched AoS would not be confused. That said, Coulson could have been there to hand over project Theta, and had a quick moment with the team with some quip about how they revived him.
I also read Whedon thought it'd be cheap for him to pop up again "here I am!" when his sacrifice was the big thing that brought the team together in the first movie. Though I agree it's hard to believe people like Stark, Black Widow and Hawkeye wouldn't have noticed he's still alive. Maybe they were all working for boat SHIELD instead of basement SHIELD.
I am surprised that I haven't heard any Whedon-hater complain that he put a character into the story that essentially looks at the audience and literally says "I bet you didn't see that coming" as he is killed off. LOL.
That was a nice touch.