Okay, I'm going to say my opinion:
I think Star Trek deserved the Makeup award. I mean, comparing both movies, Star Trek's makeup was way more complex than Suicide Squad's. When they showed small clips of the movies, I could easily tell that Star Trek would win it, but that didn't happen.
Anyways, I'm really glad that Fantastic Beasts got an award, even though it was for Costume Design. I loved that movie, even though it was kind of a related to Harry Potter. I was practically silently screaming.
I get that The Jungle Book won the Visual Effects award, and I applaud them for that, however, (of course, in my opinion) I think Doctor Strange had better effects. I mean, of course creating the animals must have been hard, but I thought that the effects from Doctor Strange were more complex. I haven't seen the whole movie, but from the small snippets that I caught, I could tell that those effects weren't easy to create.
I haven't seen Piper yet (the animated short film), but I liked that it won since it looked adorable (from the small clips they showed). I would like to see it sometime!
I may be biased about this, but I'm glad that Zootopia won the Animated Feature. However, I haven't seen Moana yet, so I may be biased.