It probably won't amount to much, but Mary Jane letting slip 'I love you' as Peter cures the Spider plague en mass can easily be taken as a wink towards those still sore about One More Day (Everyone).
Sucks for Peter, but the fans are very happy to see Carlie dump him, though more for the fact that they're no longer together than him doing anything particularly dickish. And thing is, he didn't - Carly broke up with him because he hadn't told her that he was Spider-Man, and for no other reason.
The Jackal masterminding the entire scheme for the purpose of harvesting Spider!Queen's DNA. Of course, given his history, it was very likely everyone at the very least JOKED the Jackal killed was a clone.
Mary Jane gets spider powers just as things are going to hell. Her first act with powers is to rescue defenseless civilians and lead them to safety, whereupon Reed Richards tells MJ that she doesn't need to worry about transforming at the moment. So MJ rushes off to join the super heroes in the battle against the Spider Queen, rescuing Peter and inspiring him to use his brain. Once Peter thinks of a plan to cure the citizens, MJ bravely defends him from the spider monsters. The entire reason the good guys won this one? Mary Jane Watson.
Becomes even more awesome when you analyse everything to do with the citizens gaining powers. When the criminals and thugs of the city start rioting with their powers, MJ, while only human, goes out of her way to save a small child without any powers, which nearly gets her raped by a Spider!Thug. The general population, upon gaining powers, fall under two categories: Abuse their powers to pillage the city, or laze around on their behinds until Peter gives a rousing speech to motivate them to prove to the world that New Yorkers are great people. Carlie Cooper however, upon gaining powers, goes out to save people... but not because it's right, but because it's really fun to do so. So, while the city is either rioting, in need of motivation, or using their powers for fun, the only person other than Peter who does anything because its right, powers or no powers, is Mary Jane Watson. And that, ladies and gentlemen, is how Dan Slott apologizes for what he's had to do under Joe Quesada's thumb.
Y'know how the citizens of New York are generally ungrateful to Peter/Spidey, even if he saves the city on a regular basis? Well, Pete did a damn good job in stopping the crisis that the city that New Yorkers become pretty damned happy with his heroics.
Even better - Mayor J. Jonah Jameson made the phone call for this to happen, fully acknowledging that the wall crawling menace fully deserved the credit of saving New York.
The entire climax is an escalating series of crowning moments:
As all hell is breaking loose, the combined forces of a restored Kaine in Spidey's Sonic stealth suit, Agent Venom, the Avengers, the Future Foundation and all the major heroes battle it out with a giant spider monster version of the Queen while Spidey uses his smarts to commandeer Doc Ock's mini-robots from a previous story to administer a cure to every infected person (thus reducing the Queen's power) with a spider-powered Mary Jane fighting an army of infected to protect him. As he continues to cure the entire population, Peter laughs and declares that just this once, he's going to save everyone.
Flash Thompson, the new Agent Venom, standing side-by-side with Steve Rogers himself as they start the final battle with the Queen.
Commander Rogers: You still with me soldier?
Kaine, long hated for being the obligatory Nineties Anti-Hero part of The Clone Saga, uses his new Spidey suit to cancel out the Queen's sonic scream, and his new stingers to do what Peter Parker never would, and end the Queen's life when Peter manages to weaken her, while declaring to all wondering who he is that "I am Kaine!" And before Madame Web can claim that clearly he was the Spider-Man she foretold would save the world from this threat, Kaine states says everyone that he only could do it wearing a suit Spidey made, using a move Spidey perfected, at a moment that Spider-Man created for him. As far as Kaine is concerned, as well as everyone else, the one who is responsible for the Queen's defeat is the one and only Amazing Spider-Man. And that is how you rescue Kaine from Scrappy status.
Eddie Brock, Anti-Venom, is confronted by Reed Richards and is told that his symbiote can heal those that are infected by the virus. But, if he does so with so many? The symbiote would die. Eddie takes it in stride, goes to a church and gathers everyone he can who were affected and cures them. The symbiote did die, but Eddie left a hero. This storyline was pretty much the Earn Your Happy Ending for Pete, Kaine AND Eddie.