* AlwaysChaoticEvil: Many of his villains. According to Ennis himself, this is a direct reaction to the concept of "JokerImmunity" that pervades the comic-book medium. He once phrased it in a ''Wizard'' interview as writing villains who are "worth the bullet"; he doesn't enjoy works in which the hero proves his moral superiority by letting the villain live, as that's usually a choice on the hero's part that will get someone else killed at some point down the road. Of course, this ends up with the side effect of most of his villains being one-dimensional and poorly written, not to mention redundant as they end up basically all the same.
* CrossesTheLineTwice: Ennis has an extraordinarily dark sense of humor and a penchant for sex jokes, which turns many would-be readers off from his work. While he's not unusual in that regard among other UK-based writers (Warren Ellis in particular can give him a run for his money), Ennis is the one who's built a reputation off of it.