Batman Begins, for example, gave no indication that Ra's Al Ghul was really Liam Neison.
Ask yourself this, when has there ever been a major twist is Spider-Man let alone a reason to misdirect anyone. True, there is no reason for him to stick to the comics...but hasn't he? Most of the origins thus far, most of the general storyline, most of the plot is all comic book based. Venom's origin, Harry taking revenge on Pete, Sandman gaining his powers, Doctor Octopus fusing with his arms, Green Goblin becoming that way from fumes, even Peter Parker's origin as Spider-Man...all correct, even moreso than Batman Begins which closely ties everything to Ra's (and removes a lot for time reasons).
At the end of the day it's a lot harder to explain Flint Marko's character as the killer. A man who has quams about stealing cars but not about killing

. Or someone who has quams about killing but not about stealing. It seems to me Flint is very much a victim of circumstance, just like Peter, just like Harry, just like Eddie, just like MJ and just like most people in Raimi's movies. Also he never once strikes you as a killer, with that scared look on his face. That calm, almost reasoning look on his face with Ben.
I agree with Spider-Man those wireimages paint a different story...so does Spider-Man 1