First, it would be a mistake to do a hard reboot. I know they don't want to be accused of imitating their Marvelous competition, but Marvel's approach to time passage/continuity is the only one that works for the DC/Marvel style comics universes. Soft, floating time is best. Try to avoid any well defined time skips. Everything happened, less popular incidents get either not referenced ever again or retconned. That being said, a the New 52 approach would have been the way to go if they'd had their act together. Sadly, they didn't.

- They had no plan. Everything regarding what did and didn't happen should have been mapped out before. They previous iterations of Titans happened, then didn't. And so on, and so forth.
- Making Cyborg a founding JLA member. Making him a present-day member who more or less graduated from the Titans would have been far better.
- They tried to bring back the GA characterization of Superman, in spite of the fact that the characterization didn't stick around all that long and was ultimately unsustainable. They made Superman, the most iconic if not best-selling character in their stable, much less likable. They ditched the Lois relationship.
- They made fundamental changes to characters to the point that they were only that character in name. Tim Drake, Kid Flash, Wally West, arguably Martian Manhunter.
- They leaned into a lot of the more XTREME, unpopular 90's elements. A lot of stuff intended to be shocking.
- Very good costume changes, a lot that were ok, and some that were terrible. Part of the whole change for the sake of change, really.
- What they did to the JSA and how they handled Earth 2.
- Leaning too hard into Darkseid and is crew. Darkseid is too awesome to use constantly. Unless you are going to have a Fourth World line, which I would favor, it should always be noteworthy when his crew comes calling on Earth.