I thought there were a lot of great, little moments in Punisher: War Zone, but, for me, the best part was when I realized that they were essentially serving up a bat-shit, gonzo version of Tim Burton's Batman.
Like - Jigsaw's origin sequence. In Batman, it's an accident that Jack Napier falls into the vat of chemicals that start his transformation into the Joker. But Punisher drops Billy into the recycling machine - and turns it on - on purpose. (Blowback is one of the themes of the movie.*)
I don't think the movie ranks with the best Punisher stories from the comic books (the Ennis/Dillon "Welcome Back Frank", the Ennis/Robertson Born, the Ennis/Corben The End, the Grant/Zeck Return to Big Nothing, the best stories from Mike Baron's run), but I think it's a pretty good Punisher story and more faithful to the comics than the last Punisher movie**.
But I don't think there are many - any? - super-hero movies that manage to stand alongside their best super-hero comics counterparts. Even something as great as Tim Burton's Batman Returns pales next to Frank's The Dark Knight Returns. And no screen version of Superman has come anywhere close to Morrison's All-Star Superman or Moore's Whatever Happened to the Man of Tomorrow? let alone Siegel's "The Death of Superman". The Spider-Man movies are enjoyable, well-made action/adventure/fantasy movies, but the Ditko/Lee and Romita/Lee Spider-Man comics are among the greatest works of American popular art.
One of the reasons I balk at ideas like the ones Tucker proposes in this post is that super-hero movies already give us super-hero stories with all of the idiosyncrasies filed off.
*"Blowback" would be a good name for a Punisher villain.
**I like the last Punisher movie, too, but for different reasons. It a more of a standard, but well-done, action B-movie.