Even better question: why didn't they write a tight two-hour movie instead of a cluttered three-hour one? Each of the four pre-Avengers MCU movies was about two hours even, and none have so far exceeded 2:30 (not counting five minutes of end credits). Raiders of the Lost Ark is 1:55. The Wrath of Khan, 1:53. Hell, Casablanca is only 1:42.
Movies generally don't end up being three hours by accident. Filmmakers are fairly savvy about scripts' page-to-minute ratios, and goodness knows the studios have the money to record and edit table read to time things out. Heck, combine that with the storyboards that are being drawn anyway, and you can pretty much preview your own movie. That the studio apparently didn't demand a page one rewrite when Snyder and Co. presented their three-hour script was an, if not the, early problem.
As someone that has some filmmaking experience, I'll argue that running length is always a variable when it comes to workprint edits. My films are always longer than the script. Sometimes by a lot and sometimes only a few minutes longer than the projected length. It is possible Snyder and company always figured the movie would be long. If you read an interview with the film's editor, David Brenner, it sounds like everyone involved in the film knew it was always going to be long, too.
Snyder has gone on record saying the Ultimate Edition was his preferred version of the film - the version he wanted to release. It sounds like for a long while that version was always going to be the one intended for release until some executives at Warner Bros. got nervous and ordered trimming. If you watch the Theatrical Cut, it reeks of last minute tinkering. Scenes abruptly transition from one to the other, with very minimal flow from one scene to the next. The Ultimate Edition actually feels like a cohesive film with a narrative that makes sense and editing transitions that don't make you scratch your head in literal confusion.
I still think the film as a whole has some fundamental story problems, but the Ultimate Edition is a much stronger film. I don't think all of the blame can be laid at Snyder's feet, at least not for the Ultimate Edition. I think WB should have committed to the three hour version if that was the version Snyder always intended to make. And yes, while most of the Marvel films are two hours, they had the advantage of being standalone adventures introducing solo heroes. Batman v Superman had the almost insurmountable task of being a sequel to Man of Steel and introducing a new Bruce Wayne, Alfred, Lex Luthor, Diana Price/Wonder Woman while simultaneously planting the seeds for the Justice League, future storylines/installments and addressing fans' concerns from the last movie. I'm not sure in which universe Batman v Superman could have been a good two hour movie with all of that to address.
Perhaps if WB actually made a standalone Superman sequel, rebooted Batman and perhaps made the Wonder Woman film before tossing them all together in one film that was suppose to set all this up, a Batman/Superman film could have been 2 hours. However, that's not how WB went about doing this, so alas.