Honestly I think it actually has A LOT to do with the fact that kids these days literally thought the movie looked stupid. That was I was hearing from people around me anyway. Many of kids (ages 13-18) that I have talked to recently and have mentioned Batman v Superman or saw the trailer at the theater said they thought it looked extremely dumb, without really giving a honest reason why. Then when the civil war trailer started up they thought it was the most entertaining thing in existence. Marvel has such a dominion right now in the comic book genre that it can pull the same exact trick as another huge franchise, but where one will be ridiculed and called "stupid, and dumb" for the heroes to be fighting, Marvel can be called "spectacular" for doing the exact thing.
Well, to be fair, a normal, non-superpowered guy going toe-to-toe against the fucking SUPERMAN is inherently kinda dumb on the face of it, even if that "normal" guy happens to be Batman. I'd imagine THAT'S the basis of the average moviegoer's dismissal of the concept in general. Whereas, in comparison, the opposing sides in the MCU's civil war are FAR more evenly matched, so therefore the general perception would be that the core of the movie is MUCH less preposterous that that of the submission from its Distinguished Competition.
I do find it odd how people claim the things we expect out of Superman would no longer work in a live action film when Captain America has been doing well at the box office doing the sorts of things people claim would not work for Superman. Which is kind of a shame because the big blue optimistic boy scout vs a bitter older pessimistic Batman could have been a really great contrast for a movie.
This, honestly. The scenario is ridiculous because it always depends entirely on Clark's morality stopping him from just crushing Bruce's head into a paste half a second into the fight.
Batman being basically the weakest member of the Justice League protected only by plot armor/being crazy prepared is a running joke in comic book fandom. But it flies because comic book readers know the context. Now moviemakers are asking your average movie spectator to buy into the same premise and look past this debalance... while many of them audience not being avid comic book fans.