It's concerning that DC / Warner Bros. have lost 2 directors on this project. I see the term "creative differences" and the first thought that comes to mind is perhaps the scale of this film is really daunting / intimidating.
If you're familiar with the Flashpoint storyline in the comic books, you know that things come to a head (to put it mildly) between the Atlantean and Amazonian kingdoms. However, there is a darker theme here, and that deals with undoing a heinous crime involving the death of a loved one. If you could undo it (a.k.a. change time), would you do it, consequences be damned?! To a large extent, the comic book kinda glossed over this part and focused instead on the war. The CW's TV series dealt with this in a bit more gut wrenching detail, and it was emotional to watch. (The words "Run Barry, RUN!") will forever live with me...). Once DC saw (and understood why) the success of Wonder Woman, they probably realised that they need to capitalise on emotionally driven stories more. Batman vs. Superman did have some of that, but it was clumsily done. Wonder Woman nailed it.
It might be possible that the 2 earlier directors came into this project expecting to do a "straightforward" super-hero movie, i.e. origin story, hero tries to understand and control his powers, all the while trying to stay sane and live a normal life, attracts the attention of a villain (Zoom, the Rogues, Abracadabra, take your pick), suffers a defeat or 2 before ultimately snatching victory from the jaws of defeat, gets the girl, and sets up something of a story line for the sequel. DC (via Geoff Johns, most likely, as he wrote Flashpoint) wanted to delve a lot deeper into not just the Flash mythos, but also the DC mythos, and such an undertaking scared the crap out of the directors. I see this film as another Justice League movie, though where the Flash is front and centre.
Coming back to my theory about DC / Warner wrapping emotionally driven stories in super-hero wrapping, the Flashpoint story line deals with the familiar themes of redemption and loss, hate and anger, this could be DC's most ambitious movie yet. More ambitious than the Justice League film, and anything else on its slate.
Whilst there's no director attached to this film yet, I have faith in Geoff Johns. He wrote some of the best Flash stories IMHO (superseded only by William Messner-Loebs and Mark Waid). The reason his stories were so good? They didn't lack humanity. It wasn't only about super-heroics; he tapped into the mythos and what people can relate to. The Flash is my favourite super-hero (specifically the Wally West version from the comic book). I'm confident that DC will do this story and hero justice.