BvS had two major issues to me - that it was still dominated by Warner Bros.’s desire for a “versus” movie rather than a team-up, and that Snyder seems to be uncomfortable with Superman/Clark in “standard mode,” and seems to struggle with him a bit.
Snyder’s Justice League is better with Superman than BvS, but Snyder achieves that by “painting around” Clark more than “painting” Clark himself - he keeps him out of action for the bulk of the film, and he’s more taciturn than he was even in the Whedon cut. And I think that’s because Snyder’s very much a Frank Miller-type of comic fan, and just struggles to grasp exactly how to grapple with both Superman and Clark Kent. Cavill himself isn’t ever a weakness in these films, but I feel like some of Snyder’s preference for weary cynicism even in idealists, and a distrust of Superman being an altruistic hero, caused the desire to deconstruct him in BvS in a somewhat sloppy manner.
But beyond that, WB’s wanted a “versus” film since the 90’s, even though there’s a much more proven track record in just doing a team-up between the two. That meant they wanted a climax that would at least still start with them as enemies, which meant a build of them both being enemies, and that just caused a cascading issue throughout the film for both.