My memories of the New52 already started fading and I didn't follow every series - which means that I may be wrong. But there are a lot of plot points which were never fully developed within the New52. Here is a list, add more if you want.
1- The mysterious "they" Pandora referred to at the end of Flashpoint - the villains who broke in three parts the original timeline.
2- The fight which occurred between the Martian Manhunter and the JL, and prevented him from joining the team.
3- The mysterious foreshadowed by J'Onn when he said "they're not ready" (he referred to the heroes) - I don't remembers the issue, though.
4- The Trinity War. Boy oh boy, what a mess, loose threads everywhere. Just a couple come out of my mind, that is, why the Society created Dr Light and why the Society made Superman KILL Dr Light - but there are plenty more.