Feel free to simply list your picks or include some reasoning behind them.
Here are just a few of mine:
*Zero Hour: Dan Jurgens' original idea for the outcome of ZH would have been far superior to what we got: a new Earth-Two that would have become home to the pre-COIE Earth-2 characters.
* The awful treatment Superman's continuity received during the first eleven years of the new century.
*Identity Crisis.
*Infinite Crisis: Kal-L and Lois survive, Superboy isn't a villain, the aforementioned return to restored versions of their Earths, a new Multiverse exists based on the separation of the five Earths combined in COIE
*Post-IC Superman: Secret Origins is released first, followed by Up, Up, and Away, Escape From Bizarro World, Superman and the Legion of Superheroes, and Brainiac. Johns would stay on and write a much better version of the New Krypton story as well as the Sun-Eater story he references in Secret Origins. Releasing these stories in this order would have fully established the new status quo for Superman and would have helped Johns and Busieks' runs overall.
*Batman's evolution into "Asshole Batman," especially "Tower of Babel" and the OMAC nonsense.
* Damian Wayne surviving the events of "Batman and Son."
* Barry Allen returning and replacing Wally. Barry returning isn't the problem, it's his function that still doesn't work today.
*Flashpoint having anything to do with a reboot.
*The New 52.
*Jon Kent being aged up and used by DC and Tom Taylor as a virtue-signaling stunt.
*Clark revealing his secret identity. If anything, I wouldn't mind learning that Perry and Jimmy have known for years but have kept it secret because of their love for Clark and Lois.
*No Bendis on Superman and Legion. Give him The Question or someone else and keep him out of superhero stories.
* No Tom Kong on Batman and no Heroes In Crisis.
* Alfred's death.