When I first reacted to Civil War, I couldn't fully put my finger on what bugged me about it. Now I can.
It's that it puts so much effort into setting up only to subvert the whole "of course they'll come together in the end" expectation of a versus story. I know the comic didn't end with them coming back together, well I don't like the Comic either but at least the Comic didn't have a subplot dedicated to baiting and hooking fans who like that message.
And it's insulting to me in regards to how this movie is compared to Batman V Superman. BvS may have a darker tone. But BvS ended on a message of hope and unity that Civil War literally said "____ You!" too.
In BvS things were darkest just before the dawn. Civil War was just another Marvel movie all about setting up future movies. BvS had a couple scenes that were there just to set up future movies, but with Civil War the very plot itself was only made to be a cliff hanger.