If it's a new trilogy, I also think SPidey vs New York is the best plot... Jameson vs SPiderman... I like the JJ becoming manwolf and dying and JJ getting revenge with scorpion is a great way to go... obviously it's far fetched... but I wanted to include as many people as I possibly could...
SM4: Villains: Lizard, Kraven, Cassidy (Carnage cliff hanger)...
Plot: Peter races to save his former professor and mentor from the greatest hunter in the world... in the mean time, a psychotic killer is on the prowl after breaking out of jail, and when he stumbles upon the symbiate, he becomes somthing else entirely... can this "carnage" be stopped, or is one of Peter's friends destined to pay?
Ending: MJ is off to L.A while Peter gets even closer to Gwen... Lizard/Conners returns to normal after he is given a cure... Kraven is soon hunted himself and arrested as his hunting days come to an end... Cpt. STacy (if still alive at this point) is killed however when Spidey dodges Kraven's spear but unfortunately... Stacy gets the brunt of it... Cassidy takes John Jameson hostage and kills him after escaping the police... the symbiate finds him in the end as he hides in an abandoned facility...
SM5: Villains: Carnage, Scorpion...
Plot: J. Jonah Jameson, still grieving for the death of his beloved son John Jameson in SM4, is bent on revenge and blames his son's death on Spiderman... and when Gwen Stacy is carnage's latest victim Spidey takes it personally... on top of that... Jameson's former girlfriend Felecia Hardy is now the newest pray to this twisted serial killer... Felecia is soon caught in the middle and doesn't know who to trust... Jonah soon takes matters into his own hands and hires and funds the Scorpion project to eliminate Spiderman once and for all... but when Scorpion goes crazy creates havoc in the streets of New York, Jameson is left with no where else to turn... just when things are looking bleak Jameson find an unlikely ally... Doctor Octupuss...
Ending: After Gwen Stacy's murder, Spiderman is crippled and breaks up with MJ and says that it will never work, while admitting to having an affair with Gwne while she was away... The scorpion tracks down SPiderman but runs into something else entirely... and alien-like creature Carnage tears him to pieces... Jameson with nothing left... goes down to the harbor for a walk and runs into Octopuss... he meets up with our old friend... together they concoct as master plan that will appease both sides if carried through...
SM6: Villains: Sinister Six
Plot: Ock puts together a team to take revenge once and for all... Ock leads the team which includes Mysterio, Kraven and the shocking return of the Sandman... recruited to the team are two former employess of the same electronic company, currently working together as partners in crime... Max Dillon, a former electrical engineer who undergoes a horrifying electrical accident, and Adrian Toomes, a man obsessed in flight... make way for electrode and vulture as they join the Sinister Six...
Ending: Ock pairs with Mysterio and they find a way to ressurect the Sandman for additional arms... in addtion... two criminals foiled by SPiderman earlier join the team as well... ala Electro, Vulture... these two help Kraven escape from jail and the Sinister Six is formed... but when Ock can no longer control this team... Jameson realizes he was wrong and urges the city to bring down what he partially helped to create... Spiderman and the NYPD team up to try and take down the Sinister Six... SPidey finds an unlikely ally in the Black Cat who is of additional help... Black Cat kills Kraven... Mysterio is taken down by the police... Spiderman finishes off Sandman... and Electro and Vulture turn on Ock when they realize their plan has failed... NY is saved and Pete/MJ even get back together again...