I feel this thread is kind of handicapped because we still don't know what the original story was. Circumstantial evidence implies that it was radically different, and possibly a rushed script, though we don't know that. Still, here's my ideas, trying to save what's still in the film.
-First major change: open at security briefing trying to address the repeated failures to stop the violent and dangerous expansion of a heavily-armed organization called... Intergang. They're affiliated with numerous terrorist organization and LexCorp, and seem to be filling the latter organization's power vacuum in the gun trade with no, terrifying weapons and allies that astound everyone.
- Enter Amanda Waller, who begins her briefing scene from the film. We receive the quick clips covering everyone, but focusing on Deadshot and Harley (also, Boomerang's scene is now on camera and shows him being humiliatingly subdued with his pants down, since his whole thing is he's an ass who keeps going no matter how foolish he becomes, and Harley is mentioned as being enhanced by "a Eco-criminal associate.")
- We speed up an abridged version of the Belle Reve and recruitment scene, focusing in on Flagg and Deadshot's scenes together, though now Flagg seems far more respectful of Latwon as well as extremely morose and a bit less hostile to the idea of the Squad When Waller reviews Quinn, she is seen getting a text message, which we don't have answered till later, though Harley clearly figures out something's going on.
- Second Major Change: we have a relatively short, 15-minutes Max, sequence where the Squad takes on Intergang. The group's concept is proven lethally effective here, with only El Diablo refusing to contribute, and Flagg's girlfriend unleashing the Enchantress to annihilate some mysterious, huge, and disfigured creatures in trench coats (Parademons). Slipknot is also killed here, in circumstances that seem to show that his training is greater than Boomerang, but Boomerang's cunning takes him out.
- The Intergang scene ends with Enchantress fighting an ally of Intergang, who we fans figure out is a Female Fury. She calls Enchantress sister (putting Enchantress as an Apokilipitkan), and as she dies, frees Enchantress from one of her safeguards, starting the conflict from the finished film, though now restructured as the team's extraction being put off until they rescue Waller and get put back in their box.
- We now enter the finished film's sequences, albeit modified. For instance, Croc is saved by El Diablo's first display of powers, and they start to form a quiet friendship off their origins as petty crooks with conditions that gave them power-- but with drawbacks. Harley gets more scenes of prodding everyone, and she and Katana begin a verbal duel where Harley eventually reveals that she thinks Batman sent Katana. When Deadshot bucks Flagg's authority, a desperate-to-save-June Flagg references Lawton having killed his brother accidentally, like in the comics, to get him to shut up.
- Our group is thus tense but bonding when they get to Waller, with the Joker "rescue" and Waller being the rescuee almost breaking them from Flagg's control. Joker also is more clearly abusive and evil here, and the Squad witnesses the usually tough Harley display her problems before her chopper goes down too. With Waller down, the Squad abandons Flagg, and we get the bar scene after they pick up Harley.
- The bar scene is redone a bit here, with Flagg showing up halfway through, and ordering a whiskey as well, before revealing he's the last survivor of the Squad's predecessor--Tier 1 operators who escorted Echantress, with a heartbeat bomb planted to kill Enchantress if he dies, and that he had it removed against Waller's protests. Since June would rather die than remain Enchantress, he now regrets that decision, since hundreds are dead and she's trapped because he was a coward. He's going to free her, even if it kills him, and he gives Deadshot the letters and everyone else some last bits of their previous lives before heading out.
-The screen also contains discussion of their heroes, with the Bat-villains describing Batman in varying forms that show how they're brave in their own way for facing him, and Boomerang being mocked because no one believes the Flash story, with him going "Screw you all, I'm out of here!" And leaving.
- Diablo is going to join Flagg because he's wants to get some redemption, and calls in Croc with the debt for saving his life, though it's clear Croc wants to help El anyway. Deadshot reads his daughters letters and that makes him go (with some element of a challenge by Flagg that he's down one loved one because of his skills and may lose his daughter if he doesn't help) and Harley follows because she's bored and has nothing to do. Boomerang rejoins because Enchantress's goons are closing off escape routes, and we get a laugh at him initially trying to sound like he came back because he likes them before giving up and admitting the truth.
-We get the fight scene, but tidied up, with Enchantress showing June's still in their by her inability to kill Flagg, and Croc rejoining the fray pissed at El's death in the explosion, finishing off the wounded Incubus by eating his heart. Enchantress is going to win when Deadshot distracts her by shooting Flagg, seemingly fatally, which allows Katana to wound Enchantress, weakening her enough for the combo attack in the film. Flagg survives because Deadshot intentionally hit him non-lethally, and they manage to force Enchantress into Soultaker, freeing June.
-Waller frees herself, holds them hostage, and we get the end of film for the characters, though now it's clear that Flagg, while not a crook like the rest, is reluctantly considered one of the gang, since they refuse to ever be put in the field without him as their liaison. We also have a scene confirming that Katana is Batman's agent, and instead of rejecting the notion entirely, he warns her not to use it against anyone lower than a meta human attack, and Waller notes that he could have sold her out, but seems to agree the Squad is needed, however much he hates the idea.