I think people are assuming what Civil War is about and then being upset when the movie is going in a different direction.  From everything I can tell, the movie is about controlling the Avengers.  It's not about superpowered people generally (screenshots of pictures notwithstanding).  Therefore, it has no reason to reference Agents of SHIELD.
		
		
	 
You've zeroed in on (what I find to be) the most irritating complaint on fan sites:'they're not telling the story right'.
 These viewers watch the show and somehow feel that, given all the time they invested, they must be entitled to have a say in the direction it takes. 
 How else could you explain the death threats to show runners?!
 That's an extreme example but on a smaller scale, simply expressing disappointment  with a creative solution is acceptable. 
Then there is a line crossed when you see a fan has clearly built up a storyline in their head canon that completely diverges from the show's narrative.
 Head canon can be an amazing thing, especially if you are in step with the writing style so that the narrative meshes with your perception of the world the writers have built.
 Not so much as to be predictable, but if you are onboard for the ride and open to be told a story, why argue with the story teller?
I can't help but liken it to a petulant child being told a bedtime story and interrupting with 'why's and 'what about'... not really paying attention to the story but more concerned with the story they want to hear.
To those childlike adults I say: let's see your script.