Superman wasn't involved in the decisions to change history, so while the character had less agency, which is usually a bad thing, in a work of fiction, it meant that the character couldn't be blamed for the decision.
Flashpoint was ultimately an unconventional Batman/ Flash team-up in which Barry Allen was able to undo a mistake he had made while changing history. So the central story was intrinsically appealing to DC fans. And the changes to the New 52 occurred as a result of a decision that's more acceptable to readers than a story in which a hero isn't unable to undo a bad decision.
The previous few years of Superman comics hadn't been that good. You had the World of Krypton mini-series followed by JMS's walkabout arc. Compare that to the Spider-Man comics, where the Back in Black arc gave Amazing Spider-Man the best sales of JMS's tenure on the title. Most readers were happy to trade that for Grant Morrison on Action Comics.
I like "One More Day" it should be left as it is
A blogger had an interesting idea: Reveal that all the changes are part of a deal Mephisto made with Norman Osborn.
It's more effective than the average solution to make OMD critics happy/ neutral.
I find it incredible that people only reach the bargaining stage 5 years later.