Originally Posted by
Dataweaver
Getting back to the comics:
I'm tired of Barry having a dead mom. He went all through the Silver and Bronze Ages, from his creation in the 1950s to his death in the Crisis on Infinite Earths, without a dead mom; and he did fine. As well, the idea that attempting to go back in time to save her necessarily makes a mess of the timeline doesn't sit well for me: in addition to the fact that there used to be a timeline where she was alive and well and the universe wasn't a mess (the pre-Final Crisis timeline), there's also the fact that the Flashpoint changed things about the timeline that saving the life of one middle-class housewife had no business changing.
And if Wally can be salvaged from the train wreck that was Heroes in Crisis, Barry can be rescued from the Flashpoint.
That said, these are comics; and as such, you don't just change it. You tell a compelling story that changes it. Here's how I'd do it:
Start with a Second Flashpoint: something in Barry's past inexplicably changes for the worst, in some outrageous manner. Killing Iris would be the obvious move here, but perhaps that would be too obvious. Whatever it is, Thawne shows up and taunts Barry about it, saying that he caused the change, and that because the Negative Speed Force was involved, Barry can't undo it without shattering the timeline like he did when he tried to save his mother. He then gloats, saying that he's going to do it again and again until Barry's life is a total shambles; and that there's nothing that Barry can do to stop him.
This sets Barry off on a quest to do exactly what Thawne says that he can't. After some investigation, he finds that there's something unnatural that entered into the Negative Speed Force at some point and imbued it with the additional ability to freeze time, which is what Thawne was talking about: attempts to change frozen time will instead trigger a Flashpoint, shattering the timeline in wholely unpredictable ways. But if that thing that entered the Negative Speed Force can be dealt with, the pockets of frozen time will unfreeze, and Barry will be able to set right what Thawne made wrong.
Barry then enters the Negative Speed Force, confronts whatever it is that has been causing the “time freezing” effect to manifest, and defeats it. When he returns from the Negative Speed Force, he then follows through by visiting each of the “frozen time” events that Thawne created and undoing them — notably including his mom's murder. This time, without the artificially frozen time in play, the timeline doesn't shatter, and is instead put right.
Barry then nabs Thawne, throws him in prison, and tells him that there's nothing that he can do that Barry can't undo; his days of screwing up the timeline are over. Maybe even reveal that Thawne is now unable to access Barry's past at all.
Finally, Barry returns home to enjoy his life as his parents stop by for a visit; or some other final event that shows the new status quo that Barry has earned.