If it's true that Lizard is the villain for the reboot, I want the story to be about finding a cure for Lizard while the scaly beast run amok New York City, and NOT kidnapping Mary Jane. MJ shouldn't even be involved in the final battle. She could be kidnapped by thugs earlier in the movie, but the Spider-Man/Lizard dynamic should just be those two.
And the whole "finding a cure" storyline could work well with this reboot, with having Peter having these abilities and struggle over wether he should take the cure himself since he wasn't able to save his uncle when he had those powers.