Let's see. Most of this has been said already, so spoiler tagged to make it easy to skip since it's a tldr post.
! How Oda handled the scene after Kuina's death. Zoro just asked for Kuina's sword and her dad's just like ok…seemed too rushed.
! How Kuro was given this "emotional" backstory on how he loves being the butler only to reveal himself to be an evil pirate. Never understood how he regarded Kaya's parents and it gave me mixed signals on what kind of person he is. It'd be like if Lucci (and only Lucci) saying how much he loves his job as a shipwright as part of his "cover" before the big CP9 reveal.
! How the Tsumegeri Guards weren't given a funeral for their sacrifice or any mention again really.
! How Enel mentioned twice on how Luffy is so fast and didn't just dodge his attacks. He's lightning.
! Pell/Skypiea guards/All the allies in Enies Lobby/Lacueva survived.
The allies I'm more ticked that they don't seem to have any battle scars. I'd think charging a government stronghold would leave more permanent wounds.
! How all the general zombies were taken out by Oars. Mentioned how that zombie scene could've been handled like the animal scene in the climax of Movie 10.
! Luffy's shadow powerup. It's more of the fact that Lola and co. knew Luffy was going after Moria but didn't bother to explain any of this to Luffy when Spoil asked for help.
! The key Hancock gave Luffy. How she got it was never explained, and then it just ended up breaking by a super accurate shot by Kizaru, which Kizaru should really be using on people's heads if he can aim that well.
! That Oda didn't show the entire stories of the Strawhat Separations. Wished he showed more of what happened with the crew between the initial separation and their reactions about the War after it happened.