- Audience-Alienating Premise: As the title of the story may indicate, the Punisher slaughters pretty much everyone in the Marvel universe. If you're a fan of Marvel superheroes, or superheroes in general, then it's very unlikely that you'd be interested in this comic.
- Broken Base: The story is lauded for having the Punisher kill nearly everyone in the Marvel Universe as the title promised, and in impressively pragmatic ways to boot, but also has a considerable number of detractors who see the heroes' deaths as being a bit contrived and the Punisher as being too unsympathetic and out-of-character to root for.
- Creator's Pet: The plot runs on the fact that Garth Ennis hates superheroes and loves Punisher; even on his best day Castle would never be able to take out a fraction of the heroes and villains he does here. For instance, Spider-Man, Frank's first kill, is strong enough to flip train cars with a finger flick, fast enough to somersault around lightning bolts, and skilled enough in hand-to-hand to go toe-to-toe with Captain America. That's not even taking into account his Spider-Sense, which would warn him of any hidden danger and make it nearly impossible for a normal human like Frank to touch him, let alone kill him.note
- Critical Research Failure: In addition to the advantages Spider-Man has listed under Creator's Pet, there are a few other characters killed by the Punisher with powers that shouldn't have made them that easy to kill.
- The Punisher kills the Hulk by waiting for him to turn back into Bruce Banner and then shooting him. The problem with this is that Bruce has been known to reflexively transform into the Hulk whenever his life is in danger... even from himself.
- Wolverine is killed by being reduced to a skeleton after being electrocuted, when his healing factor has been shown to be capable of restoring his body after taking that much damage (and in some cases even almost to From a Single Cell levels).
- Among the X-Men characters the Punisher killed by luring them to the moon and nuking them are Apocalypse and the Juggernaut. The former is immortal, while the latter is incapable of being physically damaged (there is a reason they say nothing can stop the Juggernaut, after all).
- Also the fact that much of the Superheroes that Punisher killed should be invincible to the point where "bullet-proof" would be a moot point. One example being Ghost Rider, at least according to a splash panel of his kill counts, who are basically a Spirit of Vengeance who can't be killed with conventional weapons.
- Crosses the Line Twice: The Punisher gets arrested because he shot the Kingpin's head off... and then got stuck when Fisk's corpse fell on him.
- Darkness-Induced Audience Apathy: The main premise of this comic is that the Punisher kills every superhero and supervillain for the crime of the collateral damage of their actions hurting people no matter how hard they try. Obviously, not many comic readers would be able to stomach a story that bleak.
- Moral Event Horizon: If you're a detractor of this comic, the moment the Punisher's actions become inexcusable may depend on which hero he massacres that you like the best, since he keeps on killing them under the assumption that they have no concern for the innocents they unintentionally harm in the crossfire of their fights against evil and doesn't stop until all of them have died, not considering that they are people too until it's too late.
- Unintentionally Unsympathetic: For many of the story's detractors, the Punisher comes off as unsympathetic in spite of retaining the element of losing his family in his canon origin because he keeps on murdering superhumans at the behest of an overzealous organization blinded by their desires for revenge against the harm the heroes inadvertently caused them. Even his realization that his last kill Daredevil is really his close friend Matt Murdock and his decision to not continue working for the organization and even calling them out when they want to keep him around to kill any new supers (not unsubtly implied will include children) that will inevitably pop up has been criticized as being tacked-on as a last ditch effort to make the reader feel sorry for him in spite of his actions.
YMMV / The Punisher Kills the Marvel Universe