I don't really like the idea of tombstone but I have an idea that could work well.
like one of you said tombstone should hire Kraven I agree.
I can't think of anything for peter parker story wise, so this will all be spider-man stuff
they could have spider-man have a big fight with Tombstone and his gang basically beating them up, and spidey will think its the end of that. As he leaves tombstone yells "this isn't the end of this!"
Then he's after The Lizard to try to stop him gets beat by the lizard meets Kraven who is hunting The Lizard and they both attempt to work together then basically Kraven is hunting the lizard. The Lizard throws Kraven knocking him out and and flees away from the two. Spidey chases after into the sewer where The Lizard turns back into Dr. Connors. peter doesn't know what to do but brings the passed out Dr Connors to a hospital.
after this spider-man goes to dr connors lab at night where he is working to try to confront him about what he had seen and try to help him, but he turns into The Lizard again and flees, spider-man goes after him and then runs into Kraven once again. Spidey tells Kraven to help him stop The Lizard but says "we can't kill him he's a friend" then Kraven responds "thats to bad, but he's not what I'm hunting" and attacks spider-man.
big fight ensues
spidey gets knocked out
and awakes in Tombstones lair and takes some of Kraven's potion that gave him super human strength then they have a fight similar to the goblin fight at the end of the first movie where spidey get beat to a pulp. Before tombstone can kill spider-man Kraven knocks him out.
revealing that he has bigger plans. and reveals that he has defeated The Lizard showing that he has Dr. Connors tied up. he tells them he wants more power he wants Dr Connors to make him something even more powerful so that he himself can kill spider-man in a fair fight. he offers spider-man his potion while Connors works on the potion. Spidey says "I'm not going to fight you, I won't kill you" and Kraven tells him that "when you don't kill me the lizard will die" referring to Dr. Connors.
when the potion is ready Kraven attacks spider-man and Spidey just defends himself, when Kraven realizes he still won't fight him he takes a knife to Dr. Connors arm and says "i think both sides should match" Spidey infuriated fights Kraven.
big fight yadda yadda yadda
Spidey beats kraven, but does not kill him, Kraven eggs on Spidey to "finish what he had started" and he refuses then pulling out a gun. Spidey thinks he is going to shoot Dr. Connors and ready save him but then Kraven pulls the gun on himself and states "then i'll finish it" shooting himself in the head.