The movies are the Cliff's Notes version of the events in the comics, with minor adjustments. I'd rather that they focus on the important characters and events rather than give every supporting character the full fleshing out that they had in the comics.
They're not always 'Cliff notes' versions. Sometimes they expand and give us scenes that perhaps should have been in the books, but were not.
The big one in spider-man is showing how he got to teh stage of being able to swing on his webbing, not covered in the early spoider-man books at all, he just started doing this highly risky, extremely dangerous stunt.
In the movie they gave him a plausible reason for throwing caution to the wind after his first failed attempt, the desire to get his uncle's killer superceding any doubts or fears.
Same kind of thing with Batman Begins, we were given more insight into why he does not use a gun in his vigilante crusade, instead of 'I don't like guns because they were used on my family.'
We actually saw him go through a stage where he thought of using one, far more realistic and potent.
The movies don't always have to be cliff notes, but I know what you mean by that, and characters such as JJJ can be lfeashed out just with an extra scene or two, or even just some more dialoge and actions that is relevant than than just for laughs.
edit: and as for JK Simmon's capabilites...he is one of the best actors on the planet, no exagearation needed, the role of JJJ, even if fleshed out like the comics, is kind of beneath his capabilities, but he seems like a guy who likes to have fun with his characters, so I'm not surprised he took the role, he's not any kind of acting snob, so we should be grateful that big time talent take the time to give us our beloved characters in small cameos.