The fact that Game Freak refuses to explain a lot of game mechanics. They don't say anything beyond cursory details about EVs, IVs, and a lot of breeding stuff, like egg groups and what the Destiny Knot does. There are also some other, smaller things, like the game never telling you that some Zygarde cells can only be found during certain times of day. I know you can just look most of this stuff up, but that's not good game design. And apparently I need to be taught how to catch Pokémon for the twentieth time.