you know who, might work within the lizard story
Morbius (I actually don't really like him for a movie villain, but..)
if Connors is experimenting with a lizard DNA project of some sort, and one of his students or colleagues (Micheal Morbius) finds out about his research (trys to steal the idea) and recreates it with using bats instead of lizards (believing, that it will be a scientific break through, that will make him famous, or whatever, idk) something goes wrong and he's turn in to a genetic (human bat) vampire
it would tie in with out a completely separate subplot, that would be needed to introduce other villains
ideal cast- Jared Leto
as for from the list
Scorpion- could be good, JJ founds the creation of him to stop the lizard (to be seen as a hero, and discredit spidey at the same time) and secretly planning on having him go after, and kill spider-man as will
Vulture- it would give the movie that from above and from below, element, with him fling in the sky, and lizard hiding down in the sewers
his story wouldn't real have a connect to either spidey him self (until their first encounter, when spidey tries to stop him form doing whatever) or would it tie in with the lizard story, (or at least, not in anyway way I can think of right now), but, would still be cool
Kraven- obviously, a giant man lizard, would peak the interest of the worlds greatest big game hunter, which would work good enough for his tie in to the story