I could actually only come up with 4 minor tweaks. It was such a good movie! Many of the complaints I've seen from other people don't hold up for me, because they are either just a difference of opinion ("make it more fun") or because that person has missed the point ("why would Lex release Doomsday?").
It would have been nice to see an additional scene of Clark Kent investigating the Batman (might be on the ultimate cut). I also would have liked to see another early set-up scene of Martha Kent (also maybe on the ultimate cut). I thought Lois should've warned Martha when she figured out Lex knew Clark's identity (maybe she did, just off screen). And I thought the placement of Wonder Woman opening the JL files interrupted the momentum a bit (but I liked the way they handled JL overall).
Check out my podcast breaking down each scene of BvS.