WB clearly micromanaged him with Justice League (to the point where they invited press to the set to show them this time there'd be more jokes!), and probably should just have let him release the 3 hour cut of BvS in theaters.
That said, everything about BvS screams of Zack Snyder, for better or worse. That is his vision for the DC World. As
@Detective Conan said, including Batman in the sequel was his pitch. Affleck as the DKR-inspired older, jaded Batman has Snyder all over it. Now, maybe he and the studio were aligned on this (as Affleck had golden boy status there at the time), but Snyder is as big a Batfleck fanboy as anyone, and calls him the best Batman ever.
IMO, this was all a huge mistake. It's easy to see why at the time it seemed like an attractive prospect to WB. You reboot Batman (something that was always going to be a challenge post-Nolan), and you jumpstart the DC Universe in one fell swoop. It's almost hard to conceive of a scenario where something like this wouldn't have happened. But I still think Zack should've resisted the temptation and waited.
Honestly, and while this take is sure to ruffle some feathers, but I think Snyder may have sorta unintentionally flipped Nolan off with the whole endeavor. Nolan was godfathering Man of Steel, and his original intentions with it were for it to be another standalone trilogy in the vein of The Dark Knight Trilogy. He gave a whole interview explaining this at the time-- that it was an entirely unconnected to Batman, and that was the point-- it was supposed to be all about exploring this other great icon of Superman that was long past due for a modern reinvention. Nolan brought Snyder onto the project. He helped convince Zimmer to do the score. Mapped out the story beats with Goyer just as they did for the trilogy. The whole "From the makers of The Dark Knight Trilogy" angle being involved helped sell the movie to the public, and Nolan's involvement gave Zack some cover to make the movie how he wanted-- including the killing of Zod, which Nolan was originally against. Snyder was put in a great position to benefit from the TDKT pedigree, while still getting to make a very "Zack Snyder" movie where had creative say on major story decisions.
Snyder then turned around and basically decided to use this Superman movie as a means to trojan horse his Dark Knight Returns pet project into the mix, despite that being the exact opposite of where Nolan had wanted things to go. He pitched this to Nolan who had just barely finished his Batman trilogy that he had spent 9 years of his life on, who was understandably taken aback-- before ultimately wishing Zack the best and taking a big step away from DC. Even Zimmer was put in an awkward situation where he didn't want to have to cover that ground again-- to the point where he had to bring on Junkie XL to do it. Henry Cavill, while supportive of Snyder, was clearly not thrilled about being completely sidelined in what should have been his own sequel for what essentially became more of a Batman film.
I don't know. On one hand I can't fault Snyder for following his creative instincts and trying to make his dream project a reality. On the other hand, I think he and WB would've benefited from a little more patience and restraint here. I think it just would've been a lot less jarring if they didn't try to shoehorn a new rebooted Batman, the other JL members, The Dark Knight Returns, the Death of Superman storyline...all into one film. And as much as I can blame the studio for allowing Snyder to do it, these choices are mostly the result of Snyder being overly eager to "skip to the awesome part". All at the expense of Superman's character development.
I'm just speaking for myself, and a lot of non-hardcore DC fans when I say that the prospect of a modern Superman trilogy done in the vein of TDKT, with some of the same creative team involved sounded incredibly appealing at the time. Myself and friends who could not care less about the release of the Snyder Cut now-- back in 2013, we were ALL IN when those Man of Steel trailers hit. Abandoning all of that to retroactively turn Man of Steel into the first part of a "DC" arc rather than a Superman arc, just felt very cynical and cash-grabby and turned a lot of people off right out the gate.
Blegh, sorry that came out so lengthy. These are thoughts I've had for a long time on the situation that I've never really attempted to articulate before.