If I was DC's "Kevin Feige" I would have kept Man of Steel as the starting point, there is nothing wrong with having Superman be the universe's inception, I'd change some things like Johnathan's death, I would have Clark save him from the Tornado, and instead have him die from a heart attack at a later point, I'd keep the final battle against Zod in the city, but I'd add a scene where Clark tries to save some civilians caught in the mayhem only for Zod to laser them down or have him destroy a block while Clark was saving some civilians, basically make it clear that Superman does care about the population but he can't save them and fight Zod at the same time, could probably help seed the need for a Justice League so he gets help evacuating while he fights the bad guy, etc.
Next The Batman solo film. I have no problem with Affleck's batman killing, Keaton's batman did and no one spergs about him, but more importantly Affleck's Batman started killing after Robin's death, a solo Affleck film showing him meeting Jason Todd, training him, fighting crime together, and then finding his lifeless corpse would help everyone understand why Affleck's version of Batman ended like that in BvS, Batman would beat the shit out of the Joker seemingly killing him, but it would be revealed later that he survived but was put in a seemingly permanent coma.
Wonder Woman is mostly fine as is, the only change is she hasn't met Batman by this point.
Batman V Superman (I'd probably just re-title this to Dawn of Justice) Now that our main trinity has been established. I'd keep the scene where batman is powerless to stop the Superman vs Zod battle, as one of the main reasons he distrusts Superman, the other being that he is haunted by Jason's death he believes that if he had just killed the Joker sooner Jason would still be alive, so he now thinks that he has to kill Superman before he turns into *Insert your favorite evil superman here* Wonder Woman would be a "secret guardian" she has been helping humanity in secret, using her super speed, breaking security cameras and shit, so there are rumors of a "warrior godess" protecting humanity but few have actually seen her. The main villain would be Lex Luthor, like in the film Batman and Superman are at odds, because Clark disapproves of Batman's methods, while Batman sees him as a huge threat, Luthor would be working behind the scenes to get them to kill each other, like in the movie he will send hitmen after criminals batman has apprehended, probably even frame Batman for some killings so Superman decides to stop him, and meanwhile probably leak to Batman footage of Superman killing Zod, so this basically "confirms" his fear that Superman is not above killing those who oppose him. Similar to the film Lex kidnaps Martha and Lois, but the change here is that Martha is the one he throws from the roof while Lois is the one in the warehouse, so despite Superman saving Martha Lex tells him that he either kills Batman or Lois is dead, we see Superman try to search for Lois but he cannot hear nor see her as the warehouse would be lead lined and sound proofed, and in his desperation Superman agrees to fight Batman, they meet like in the film Superman still tries to reason with Batman, they beat the shit out of each other, Batman wins due to Kryptonite, as he is about to deal the killing blow Wonder Woman stops him, blocking the spear with her shield, Martha who had arrived at the scene rushes to Clark's side and Batman realizes he was about to kill a son in front of his mother, making him no better than the man in that alley all those years ago, Batman decides to redeem himself by saving Lois while Superman and Wonder Woman confront Luthor, no Doomsday here, instead Luthor had built himself a mech suit by modifying the one General Zod used, we get the warehouse scene, while Luthor's suit proves to be strong enough to engage Superman and Wonder Woman, we learn here that Luthor is one of the few people aware of Diana's existence so the suit is also intended to fight her, eventually Batman returns and by working together they defeat Luthor and lock him up.
Justice League: This would basically follow the same overall plot as Zack's version, have Steppenwolf arrive looking for the mother boxes, we are introduced to Flash, Aquaman and Cyborg, the big difference is that Superman is not dead, so he gets more screentime. And thats it for "Phase 1".
"Phase 2:" would consist of (They don't need to happen in this same order):
Aquaman: This move is fine imo so I'd probably leave it as is. My only change would be having Lex Luthor alongside Deathstroke recruiting Black Mantha for the Legion of doom.
Flash: The Flash solo movie would show him start working as a CSI in Central city, we see flashbacks to his mom's death, basically we learn more about his motivations for being a CSI and why he wants to be a hero, the main villain would be Gorilla Grodd, an enemy whose psychic abilities are powerful enough that even with Flash's speed he has a lot of trouble defeating him head on; at roughly the midway point in the movie Flash would see this "blur" remembering the night his mother died he would give chase but will be unable to catch up to it, only managing to see glimpses of a someone in yellow, I'd probably have Cyborg in a small role here as I genuinely don't know what to do with him. So in this scenario Cyborg will help create some mcguffin to block Grodd's mindpowers, allowing Flash to defeat him.
Man of Steel 2: The main villain would be Brainiac, Superman at this point has fully embraced his role as Earth's protector, besides most of the negative press about him was manufactured by Luthor, it would be revealed that Braniac was on board Zod's ship but was damaged during the arrival on earth and subsequent battle, and it was Luthor's tinkering in BvS that reactivated him, similar to his animated counterpart he seeks to assimilate knowledge and then destroy its source so it becomes more valuable, naturally he comes to blows with Superman when he seeks to "assimilate earth". Superman would also obtain some mcguffin that lets him create the fortress of solitude in the Artic, maybe he finds a Kryptonian crystal or something similar inside the scout ship.
Wonder Woman 2: This film would cronologically happen around the same time Man of Steel did, an archaeologist team gets lost in Africa, and Dr. Minerva gets turned into Cheetah by consequence of a ritual performed on her by an african shaman, the ritual was originally intended to restore the high priestess' youth, but during the ritual they where attacked by a neighboring tribe and cornered in the temple, the shaman reluctantly performed the ritual on Minerva hoping it would give her the power to survive, but instead transforms her into Cheetah and she proceeds to slaughter everyone, Wonder Woman arrives at the jungle investigating rumors of a "mythical creature set loose", she would obtain her new sword at some point in the film, and these events would also be the reason Wonder Woman did not intervene during Zod's invasion, as she was busy breaking bucks fighting Cheetah in Africa.
Batman 2: By this point Batman has gone back to being his usual self instead of being "Bat-Punisher", the main villain would be the Riddler, probable Nightwing cameo, and would most likely show Tim Drake in a minor role where Batman has been considering him as the new Robin, maybe show a scene where he is evaluating potential candidates and we see Carrie Kelly, Stephanie Brown, Richart Graustark's names pop up on the screen, with him ultimately deciding Tim is the ideal candidate, the film would focus on Batman's detective side as he solves the Riddler's puzzles while trying to locate him, and also show him fighting his goons and what not.
Green Lantern: I'll admit I don't know that much of the Green Lantern mythos so bear with me here (of course if I was actually working as executive prodicer or whatever Feige is, I'd read Green Lantern's wikipedia article at least). The film opens with Galan ur battling aliens, maybe Parademons? in any case we see how powerful and badass Green Lantern can be, but as his ring runs out of power he is defeated and forced to flee, crash landing on Earth, where he is found by Hal Jordan, and passes the ring to him, the main villain would most likely Black Hand, as I don't want to introduce the Sinestro corps or Parallax just yet. The end of the film would show either Superman or Batman (or both) recruiting him for the Justice League.
Justice League 2: the battle between the Justice League (Superman, Batman, Wonder Woman, Flash, Cyborg, Aquaman, and Green Lantern) vs the Legion of Doom (Lex Luthor, Riddler, Cheetah, DeathStroke, Black Mantha, Black Hand, and Gorilla Grodd). And ends "Phase 2"
Phase 3: as before the movies don't need to happen in this exact order.
Man of Steel 3: Bizarro as the main villain, haven't given it that much thought aside from that.
Wonder Woman 3: A loose adaptation of that episode from the Justice League Cartoon where Diana goes to the underworld, Hades would be the main villain and she would don the Golden armor to face him.
Green Lantern 2: Now he fights Sinestro.
Batman 3: Either Prometheus for a good ol' (Fight an evil version of yourself) or Firefly, Tim Drake is Robin by this point.
Flash 2: Mirror Master is the main villain, and after only being shown as a "blur" in the first movie, The Reverse Flash is now seen in full detail, but is still not the main villain.
Aquaman 2: Charybdis as the villain, Aquaman loses his hand here.
Shazam: I think the movie is overall fine, just maybe tone down Zachary Levi's comedic performance, as I feel Billy's personality shifts a lot after his transformation, going from a moody teen with a sense of humor to an almost bumbling idiot. I would shift the ending to show him meeting with Superman and getting recruited for the leauge, and in return he just asks Superman to show up at lunchtime for the ending scene where he reveals he knows Superman.
Justice League 3: Doomsday will be unleashed from his prison and engage the Justice League, of course the film ends with the dead of Superman.
Flash: adaptation of the flashpoint storyline, featuring Reverse Flash as the main villain.
Green Lantern 3: He would now fight Parallax.
Aquaman 3: He would most likely fight the Dead King here.
Shazam 2: The villain would be Black Adam
Justice League 4: Darkseid finally arrives on earth and proves to be too powerful for the League to handle, Superman is brought back to life, still don't know if I would do the whole "he wasn't really dead but in a self healing coma" or something, in any case he comes back to life. I wanted Batman to don the "Hellbat" armor with it being a suit he created with the help of the other league members since Superman was dead and for him to sacrifice his life to kill Darkseid, but now this feels like a ripoff from Endgame.