Sources: WB Insiders.
Note: None of these are my words, I only paraphrased what I had found on Twitter.
Before MOS:
Geoff Johns, Grant Morrison, Millar and other writers are invited to draft different concepts for the Superman reboot. Some are very reminiscent of Donner's Superman while some are elseworld, dark and hyperviolent like Superman living as long as our Sun and dying along with it, Krypton not being doomed, 8 hour Godfather-esque trilogy etc. In favour of MOS, WB ditches all the aforesaid ideas. Since then, the aforesaid names hold a grudge(they would later speak against MOS publicly).
Nolan after hiring Snyder, learns about the concerns being raised against the film by Geoff and gives strict instructions to Snyder to not let any outsiders enter the sets (Snyder mentions this in multiple interviews). After MOS releases to mixed reviews, Snyder continues to follow the intended vision and Nolan gets busy with his films.
Batman v Superman
It was going to be a different film than the one we got. Batman was always there, but originally... Corbos, a victim who suffered from the Black Zero Event was going to be the upfront villain, who is later turned into Metallo by Lex (official concept arts of Metallo available online). It had significantly different second and third acts. No Doomsday. All the finance/funding required for the DCEU ($1B) was successful through the addition of RatPac. It enters into production in late 2014 and something happens.
Influx of leaks coming out from Geoff John's office. Entire script is leaked to Marvel and that's how Civil War was born. (Ever notice the striking similarities between the two films and even be slightly suspicious how "coincidental" it was all? Billionaire vs Boyscout - Strategically won but morally lost, Govt. and Media witch hunting, Villain pulling strings from behind, Prominence of Mothers, African supporting characters, Bomb blasts pushing heroes etc. Russos even admit in an interview during the release that CW was greenlit only after BVS, little did fans know what happened. Marvel vs DC is not terrible at just fan-level but even worse at company level.)
After learning that the script is out, Batman v Superman gets delayed by a year. Zack Snyder tightens the crew. WB loses a lot of momentum and months are wasted on rewrites. Meanwhile, Marvel scraps its initial idea for CA3 and cribs the DC script to create Civil War. WB and Zack decide to raise the stakes. And that is how Doomsday was born. Corbos is turned into a supporting character - Wallace Keefe. All these changes and rewrites are happening along with the production simultaneously (also reported by a notorious "blogger"). More leaks start coming out from Geoff Johns' office, including the news about Doomsday (remember who leaked this news first? Which "notorious" blogger?). Marvel then announces that CW would release on the same date as BVS (an even lower move after getting their hands on the script). WB changes the release date again for the third time. Gradually, WB/DC gets divided into two factions fighting each other over DCEU. In the meantime, DOJ finishes production. Bloggers do what they were told to do. BVS
OJ is officially rated R with 3 hour duration. Zack is promised with the Ultimate Cut release and ordered to cut 30 mins of the film and secure PG 13 rating.
BVS releases to disastrous reviews. Time Warner pressures WB to fire Zack Snyder. Kevin Tsujihara refuses and instead promotes Geoff Johns and his friend Toby Emmerich to oversee the DCEU. (Later, on the original release date of Batman v Superman, Civil War releases to critical acclaim.)
Suicide Squad
Geoff Johns and Toby Emmerich order reshoots and force several changes to the film and its tone before the picture is locked (so an Ayer cut never existed). It was intended to be rated R with The Joker serving as the main villain in the third act - much similar to Rocksteady and Jay Oliva's Assault on Arkham (upon Snyder's suggestion), but greatly extended, violent and unadulterated version of the character. It went like this: Squad becoming villains by circumstances, then by duty (Amanda Waller) and later by The Joker.
After the mandate, 90% of The Joker scenes are cut(as said so by Jared himself), his relationship with Harley is changed from an abusive one, hole in the sky plot is added along with a lot of humour, serious tone is mostly eliminated, several scenes are reordered, violence is drastically reduced and the third act is completely changed through reshoots. More leaks begin to come out on the changes(remember who reported it first? Same "notorious" blogger who leaked the news about Doomsday. How did he get it? Already mentioned.)
Suicide Squad releases to disastrous reviews. Somehow it clicks with the targeted audience and brings in huge profits for WB.
Wonder Woman
WB had more faith in Suicide Squad than they did in this. Rumours start flying around calling it a disjointed mess. Patty puts out a statement and is mocked. Geoff Johns, who mostly worked with a writer, but never directly with Patty deems the No Man's Land sequence "very dark" and tries his best to cut it. Patty Jenkins and Zack Snyder fight for it tooth and nail and instead compromise with the third act. Reshoots begin and the third act with Ares is significantly changed.
Wonder Woman releases to overwhelming reviews. Geoff Johns, despite his less to negligible significance on the film, begins self-indulgent PR and takes the credit. In exchange of several leaks, he gets a "Fiege like positive outlook for the DCEU" from the bloggers. Patty slips about the No Man's Land getting into trouble during editing and fighting hard to keep it alive quickly changes her stance as it creates negative PR. Kevin Tsujihara after noticing the PR work repeats at a press event that they do not want to be like Marvel and simply tell stories that connect with the audiences as agreed with Snyder during MOS.
The Flash/Flashpoint
As Rick Famuyiwa's vision is aligning too much with the original, he is ****canned by Geoff. After submitting multiple drafts and refusing to compromise, he is then fired. Kiersey Clemons who was already cast as Iris West goes on to work with Snyder, calls her scenes great in JL in an interview, would get fired before the release with her scenes deleted as Snyder departs and makes a cryptic post expressing her disappointment on the social media. Rick would later make a comparison of Black Panther and Justice League at BO, laughing at the latter's performance and expressing his bitter experience at DC.
The Batman
Ben Affleck with Snyder at helm wanted to make a trilogy (besides the main series), where Part 1 and 2 in the trilogy would take place nearly a decade ago with the final one taking place during The Arrival of Superman. As he was very much aligned with Zack Snyder's vision, his interpretation of Batman was also going to be terrorizing and brutal, but with a lot less causalities while heavily dealing with the relationship b/w Batman and Robin/Jason Todd.
Geoff, who had already started erasing Snyder's influence on the DCEU, disagrees with Ben and forces him to change the tone (to the one we got in JL). Ben, who had already a lot going on in his personal as well as professional life decides to leave. As planned, Geoff and Toby hire a "hot name" that happened to be Matt Reeves.
Justice League
Snyder is now constantly receiving several notes from Geoff Johns and occasionally from Toby Emmerich. After MOS, BVS and JL, rest of the main series would be heavily influenced by Injustice, Flashpoint, Final Crisis and Kingdom Come with Superman as the backbone of it all (confirmed by Snyder and Jay Oliva) until it wasn't as compromises on Justice League begin slowly with soft changes. For instance, the costume of The Flash is ordered to be more in line with DCTV/CW version of The Flash. Snyder wanted it to be a homemade suit, which would later be upgraded by Wayne Tech. He was building within a building much like he did with Batman's.
Then the hard compromises begin: Resurrection of Superman and Black Suit(image posted by Henry on IG and talked about by DOP) are the first and foremost to largely get impacted as they are deemed "dark". A lot of elements around Batman are drastically altered, later the arcs and then the characters themselves are made to change with the addition of more humour(for obvious reasons). JL1 and JL2 are turned into a standalone with minimal references to Injustice, Flashpoint, Final Crisis and Kingdom Come. Later during the set visit, critics and bloggers are told beforehand to deliberately question Zack Snyder about his vision. (Some of them even mention about it.)
Filming is finally over in October, 2016. Jason Momoa shares it on IG and the crew receives some gifts from Henry Cavill along with a note thanking them for being alongside the long and hard battle. JL is screened in January, 2017. Geoff and Toby decide to release a different version for the theatrical release. Joss Whedon is hired and starts working on the changes (referred to as a "secret weapon" in an interview by Geoff and Toby). Zack continues to work on the post-production. On March 11, 2017, his daughter commits suicide. A week later, Snyder tries to immerse himself into his work but with even more compromises cited to be made, he decides to leave saying he's had enough.
Extensive reshoots are planned. Ray, Gal and Jason are against the changes. Kevin Tsujihara visits the JL editing room for the first time and calls out Joss Whedon on his "slapstick" introduction and orders to reduce it drastically.
Geoff Johns, Diane Nelson and Toby Emmerich take several shots at Zack Snyder in their interviews going all the way back to MOS. Geoff even calls the sandbox idea as his own when in fact it was all Snyder's.
Justice League releases to disastrous reviews.
POST-JL
Geoff Johns is demoted and Hamada takes control of DCEU.
Clay Enos, a close associate of Snyder, starts interacting with fans in various ways hinting at what happened BTS; positively reacting to the speculations made by fans against Geoff Johns. Ezra Miller and Ray Fisher's photographer calls Geoff Johns "scum of the Earth" and later deletes the tweet. He too positively reacts to the speculations. Outsiders who got to see the Snyder Cut start talking about Hamada in a cryptic way (against Geoff) and also confirm that the Snyder cut exists on Instagram (their screenshots are later liked by ZS on Vero).
Joss gets fired. Patty, upset with the way Joss had had handled WW in JL, likes an article on Twitter saying, "Snyder likes an article (on Vero) about Joss getting fired as a good thing for DC". Kiersey Clemons is rehired. New directors are onboard with DCEU. Snyder is reached out by Hamada. He confirms a question saying that he will be producing WW2. In late March, with all the changes happening and losing control over the DCEU, GJ expresses his anguish by changing his cover on his FB profile. He now oversees only CW/DCTV and the upcoming DC Universe Streaming Service content.
Release of the Snyder Cut largely depends on the AT&T and TW merger (which is being blocked by POTUS under anti-trust). Better grasp at what would happen might be known more clearly after SDCC and if/when AT&T and TW merger happens.
