Fridge Logic: At times it seems as if Stryker & Co. are the only ones on the scene who remember that Magneto is actually a criminal. (His first Heel–Face Turn was still in progress at the time the graphic novel was released.) It's true that during the scene in Madison Square Garden Stryker represents a greater concern than does Mags, who is downed relatively quickly. Still, after Stryker is dealt with, it's a little surprising that no one even considers arresting a man whose last public act involved sinking a Soviet submarine that threatened his attempt to take over the world.
That might be an explanation in and of itself; just try arresting the guy who did that. Magneto is one of the most powerful men in the world; you'd have to be crazy to try and take him on without some serious firepower or resources.
Another example, on a lighter note: why did Wolverine score so well in the Danger Room scenario? He didn't really do anything useful.
Because he actually followed orders. Anyone who knows Wolverine can tell you how well that usually works out.
Fridge Horror: As Storm is a claustrophobe, the small capsule she was imprisoned in by Stryker must have been terrifying to her.
Moral Myopia: Doylist example. Claremont famously had Kitty Pryde use the n-word to compare the oppression of mutants to that of black people, though in a context that accuses Stevie Hunter of mild hypocrisy when due to her reaction confronted with another minority's oppression. Considering that this is comparing a fictional minority to an actual minority, one traditionally threatened by mob violence that most mutants could shrug off easily, the line loses a lot of its impact.
Tearjerker: The deaths of young Mark and Jill, at the very beginning of the graphic novel. Magneto's reaction, when he comes on the scene, might qualify as another. One can tell this is not the first time he's seen children killed.
They Wasted a Perfectly Good Character: Of all the times for Claremont to forget he wrote Nightcrawler as a practicing Catholic... Kurt would have made a perfect counterpoint to Stryker's hysteria. With Stryker's twisting of Scripture to justify his genocidal intentions, Chris couldn't have found one point to have Kurt quote from Wisdom 11:23-26? note "But you are merciful to all, for you can do all things,and you overlook people’s sins, so that they may repent. For you love all things that exist,and detest none of the things that you have made, for you would not have made anything if you had hated it. How would anything have endured if you had not willed it? Or how would anything not called forth by you have been preserved? You spare all things, for they are yours, O Lord, you who love the living."
Values Resonance: You would not have to change much if you were to set this story in the present day.
This is probably the reason Stryker was changed to a military general in the movies. Since the movies reach a larger audience, Fox probably didn't want to ruffle too many feathers with a conservative Christian minister as a villain.