Im currently re watching The Avengers and it just made me think:
The rationale for Thor fighting Iron Man/Cap is as stupid to me as Batman and Superman fighting in BvS
The main difference is that the Thor vs Iron Man/Cap fight isn't as important of the film
It's classic comic book let's-have-a-meaningless-fight-over-a-stupid-misunderstanding-that-will-not-hurt-anyone-and-will-be-over-as-soon-as-it-starts-with-no-hard-feelings.
It was a farcical trope poking fun at itself as evidenced by the shot of Loki looking on bemused.
As MovieBob points out, there is a narrative purpose also being served there that imparts crucial information almost subliminally about relative powers in a rock-paper-scissors way as well.
Plus, they weren't trying to establish a grounded-in-gritty-realism deep and meaningful rationale over nearly 2hours as to why one would spend 2years carefully planning the murder of the other either.
So there's that.
The Avengers was a fun team bonding action romp that was mostly lighthearted with occasional serious themes.
BvS was a takes-itself-so-seriously-I-can-hear-the-aneurism-throbbing-from -over-here combination of existential crisis/allegorical examination of what would happen if 3 very powerful individuals, all afflicted with serious mental illness, decided they didn't like each other enough that at least 2 of them decided murder was their only viable option.
Including the one who's most defining character traits are: never commits murder and can be shot, stabbed, beaten, bludgeoned, have his adopted progeny murdered and crippled, his back broken-yet never breaks his code or his spirit.
Then BvS uses a magic word resolution to turn it into a team bonding action romp, almost in utter repudiation of the previous 2hrs.
In Avengers, we're meant to laugh at the (comic book in-joke) stupidity of the conflict (as well as "doth Mother (Martha?) know you weareth her Drapes? -now I'm reimagining the Batmobile confrontation with Batman asking that instead of "do you bleed")), but because of the marketing of BvS and the statements of its director., we're laughing at the absurdity of it.
Or, if you are truly a lifelong DC fan, crying at it.
I watched Civil War last night so I'm still feeling a bit emotional. I actually started tearing up half an hour in, not because of the moment on the screen (which was a funeral-not for any of the main characters), but because I felt I was watching them bury my hopes for and expectations for what BvS could have been.
If you haven't seen it and you're unhappy with BvS, all I can say is that it is a great movie, plus it changed my feelings on BvS, from primarily anger to sadness over what could have been.