How would two separate stories for the villains work out? This has never happened before. When there's two villains they always team up. I hate that. Wouldn't it be interesting to tell maybe simultaneuous stories for the villains, or go another way, where they're interwinded. It will probably be the latter.
But this is where I always saw Vulture and Lizard in a film. Toomes and Connors compete for a grant, Connors with this serum and Toomes with this wings. Toomes gets the grant and does his thing, Connors frustrated takes it himself, or develops it more to take it for himself, thus giving time to develop Vulture. He robs penthouses and banks, running into Spider-Man. Peter meanwhile deals with Connors, his lab assistant, I'd like that or work with Gwen with Connors. Later the test is successful, that night, Connors takes the serum and transforms. I always liked the scene in TAS where Peter and Debra go in the college and catch the Lizard. They can do that with Peter and Gwen. Maybe Lizard is on the hunt, spots Vulture, gets vaguly flashes of Toomes and what frustration he caused him, attacks him, Vulture escapes. Lizard retreats to sewers. I can definately see Raimi doing the TAS storyline where the Lizard picks off workers and civilians. Maybe he transforms back into Connors, not remembering anything, gets out of the sewer. The next day the Bugle reports rumors or sighting of a Lizard man running amock. Jameson tells Peter to get pictures, this is where Spidey finds Lizard in the sewers, tracking him, gets his pictures, but the Lizard transforms back into Connors, Peter finds out. Peter questions whether or not to sell the pictures to the Bugle for alot of more money or give up Connors trust. Maybe his family can be featured. Maybe.
But I don't want there to be a damsel in destress this time. It has to be personal bewteen Connors and Peter. He goes after him because he has to. Mj is in LA their relationship fine, she appears in the beginning and near the end. Maybe a funny subplot where he tries to call her but never has any change in his pocket or is about to talk to her but is interupted.