I would have rather seen Harry be responsible for breaking them out for their respected talents, and use a minature sinister six idea, but rather than six be three where spidey has to fight sandman, then rush across town and fight vulture then him be ambushed by a better designed new goblin. When he was tired and exhausted.
Series of events the way I would have liked to see them.
Harry is the main villain
He hires toomes to work out the kinks with the performance enhancers, remove the x-factor that drove his father insane.
After toomes has completed his work, harry frames him for some crime and has him locked up, to keep him quiet about his performance enhancers.
In prision Marko and Toomes are cellmates. Toomes offers to break marko out in exchange for protection from the other inmates, because toomes is an old man and cant really look out for himself.
Osborn smuggles Toomes blueprints on the wings into the prison to him, through a contact, namely the warden who osborn owns.
Toomes builds the wings and he and Marko escape.
They are approached by Osborn in disguise as the Goblin, who offers them employment if they help him with spiderman.
Toomes agrees, Marko goes on the run, similar to how he did in the movie, I would keep his transformation into sandman the same.
Sandman and Toomes would meet up when they both try to rob the same bank-or jewelry store, spiderman shows up and the two of the keep getting in each others way, and barely manage to escape.
Toomes convinces marko to reconsider the goblins offer, by telling him the money and resources the goblin has might be his only chance at being turned back into a normal man.
Osborn leads Marko along like he is working on a cure but instead sends them back out to cause as much havoc on the city as possible to keep spiderman distracted, he also reveals false information to the police implicating sandman in uncle bens murder.
I would keep captain stacey in the film and the meeting where he informs the parkers about marko, also keep gwen but mostly as a cameo. A nod to the fans.
Osborn has marko ambush spiderman and while toomes steals some equipment he needs from across the city, spiderman manages to knock marko out and turn him over to the police.
marko escapes when he regains conciousness
Osborn using the new equipment creates a bomb and plants it in the city, and then introduces the goblin to spiderman, The goblin doesnt fight him, merely taunts him, informs him of the bomb, and tells him how long he has to find it, before it goes off, he also tells him his two employees have the location to the bomb, but he has to find them first.
Harry gives a clue to the vulture and one to sandman, and sends them out into the city to wreak havoc again, Spiderman confronts vulture first and defeats him, and gets his clue which narrows it down some and then goes out and finds sandman who reveals that he had nothing to do with the parker death he was framed by the goblin, he agrees to give spiderman the clue if spiderman lets him go, spiderman is initially hesitant, but when he sees that all marko wants is to find a cure for his condition and wants to turn over a new leaf agrees, and lets marko go.
Spiderman using the clues locates the bomb which is in a hospital aunt may has started going to, for her checkups.
Spiderman finds the bomb but is attacked by the goblin before he can defuse it. Marko shows up to help, and goblin is caught offguard by the two of them working together and the sandman picks up the bomb and runs outside and absorbs it into his body before it explodes, he hardens his body and when it explodes he is spread out all over the city, spiderman unmasks the goblin to find out it is harry who has been playing him from the beginning.