1. Wonder Woman Killing Final Terrorist - Everything was epic, everything was fine.. until she levelled the side of a building to take out the last terrorist when she had already proven she was more than fast enough to have subdued him before he reloaded. I've no problem with heroes with 'no killing' rules actually killing, however it completely needs to be handled well... like Superman killing Zod in MoS I thought that was done well. This however felt like complete & utter overkill as she blew the side of the building off.. actually sitting here thinking about the scene, it's probably 1 of the few Whedon actually made a good decision by cutting a piece of it off.
2. Singing People At the Village - Felt like it lasted about 10 minutes & I didn't really grasp what Snyder was trying to convey with a lot of the village scene & the people's reaction(s) to Arthur, do they see him as a God like figure? or a savior?
3. History Lesson - I get that to serve the story, Darkseid must have been defeated & sent packing.. I also get that he's younger, weaker & lacking Omega beams from the looks of it, however even still I think he's defeated too easily, certainly too easily to then fit the narrative that he's a being they all fear so much.
4. Martian Manhunter - Felt shoehorned into the film unnecessarily.. which is Snyder's M.O., even worse than how Spider-Man was shoehorned into Civil War IMO. Completely killed the Martha & Lois scene because it turned out he was impersonating Martha in what was quite a heart-warming scene between the pair. Scene with Bruce, while I'll give him (Snyder), was cool & pleasing to see as a fan, it was ultimately pointless.. it also raises the question as to why is this the first time he's seen in his 3 films. He's seen Earth nearly be destroyed by Zod, Doomsday & then Steppenwolf, but only shows up now. Makes little sense, was clearly a rushed or at the very least poorly thought out inclusion IMO.
5. Black Superman suit - It was never established why he was actually wearing a black suit, he just wears it for reasons unknown. If I recall correctly don't they claim that the motherbox essentially supercharged him which would have better explained why the axe hitting him did literally nothing. Even ignoring all this, there's then no reason for him to still be wearing black for the climatic shirt rip.
I already somewhat know the reason why, because while him wearing a black suit was initially the plan, it was vetoed by WB before filming started & then adding a black suit for the Snyder cut was an afterthought perhaps to mainly help differentiate the 2 cuts.
6. Not Enough Superman - The movie is quite Superman centric without ever really having much of him physically in the film much like it was in the Josstice League. Superman is essentially in both cuts, relegated to the Hulk's role from the MCU in that he's essentially the big boy that shows up to whip someone's ass & I don't really like that.. at all. That being said, the scenes Superman did have in Snyder's cut were infinitely better than Whedon's & I still don't really understand why they reshot so many of his scenes as it didn't improve or accomplish anything over what Snyder had evidentially initially done.
7. Darkseid not killing Desadd - As some of you have already mentioned, I'm glad I wasn't the only one who thought Darkseid should have smoked Desadd for questioning him.
8. Knightmare Dream(s) - I mean I am intrigued by the Knightmare timeline, while at the same time wondering what the point of it's inclusion in this or BvS was. Was this supposed to set something up for a JL sequel? or something to do with the Flashpoint movie?
That's all I can really think off from the top of my head, but yeah, while I believe the Snyder cut of Justice League is now actually a good film & was infinitely better than the theatrical Josstice League, it was far from at least my own version of 'perfection'.