Why doesn't he have the skull?

Well it was the original writer's idea that Castle should spray a skull on his t-shirt or kevlar before the final showdown, Boaz Yakin fought for it until the day of shooting but producer Kamen ultimately decided against it.

http://www.dolph-ultimate.com

Skull or not, I find it kind of suspect that you go out of your way to point out how you're a big fan of the comics, but still think the movie is gold.
Or that somehow that absence of the skull improved the movie in any way whatsoever.

Here's why this movie fails, and it actually has nothing to do with the skulls.
It's the portrayal of Frank Castle.
In the movie, he's been the Punisher for years already. 8 years if I'm correct.
Yet, throughout the movie he seems like he just has a death wish. Like he's more concerned with just killing than he is with getting any kind of justice. This isn't a man on a mission, this is a man who enjoys killing and probably wants to die himself.
This is evident throughout, but never moreso than when he turns down the kevlar vest offered to him before the final shootout. That was it. That was the stupidest thing this movie did. The Punisher was always a guy who took every damn precaution available to him. He was never stupid reckless or suicidal like that. Maybe when he first started out- but not after 8 damn years of this.

He seems borderline psychotic, and thoroughly depressed.
This movie is bleak and dour for all the wrong reasons.
Instead of feeling like a comic book movie, a revenge movie, or even an action Punisher movie, it just falls in line with Cobra and Raw Deal as just another 80's and 90's actioner. As that... it's fine. But as a Punisher movie, it's incredibly far off the mark.