The Spiderman movies have definitely changed the story from the comic book. Watching the first of the film , I wasn't happy with the depiction of Peter Parker as more self-centred and vain, which is unusually in the context of the comic books. At this moment, Peter Park goes through so much crap that it's a wonder he doesn't commit suicide (it's kind of like Jack Bauer in 24).
Some factual points that were changed, which I'll agree was necessary to make a decent movie, are as follows: The Venom costume is an alien being acquired during the Secret Wars battle with the Beyonder (which was one of the best "cosmic" series Marvel has put out). Spiderman doesn't want to kill villains; even when he is beaten and pulverised, he holds back from taking the ultimate step (in fact, it is rare to show people dying in the comic books). Harry Osborn is more like the depiction of Normie Osborn (the son of Harry and Liz Allan) who is friends with the daughter of Spiderman (Spidergirl). Gwen Stacy is killed by the first Green Goblin (Norman Osborn). The people of New York have rarely been on the side of Spiderman. J. Jonah Jameson has always had a point in saying that it is people like Spiderman who create the villains. And so on.
It's difficult for me to reconcile what I know of Spiderman's history with a movie story that does its best and I admire that. A problem with the movies is that they can't intersect with the other characters from the Marvel Universe. It would be great to have movies like the Secret Wars or the Infinity Gauntlet, War, and Crusade series where a bunch of the Marvel superheroes get together and the stories make more sense (for example, explaining the origin of the Venom symbiote), but I guess that would be a logistic and budgetary nightmare.
Halfway through the movie, the story gets in line with what you'd expect from the book. The rejected symbiote bonds with a humiliated Eddie Brock to become Venom, one of the coolest villains to be introduced in the later years. The Sandman is a villain who is ambiguous. And Spiderman has a run of bad luck and is pummeled constantly but triumphs in the end against all odds.
I once wrote a review of the Batman series where I connected them to a lot of the comic books (I own a huge number of Spiderman comic books) and some other reviewer criticised my review. The perspective I offer is fairly unique: it is based on an experience I can't ignore or negative, and I think it helps place the movie in context of a long history of the books. So if you're interested in the saga of Spiderman beyond what you see in the three movies, I recommend buying some of the great story arcs of Spiderman just to see how complicated and mythological the creations are.
