First of all, I'd like to go on record as saying that I really enjoyed Punisher: War Zone. After two truly dismal attempts to bring The Punisher to life on film, this was the best yet. I'm not saying it's a great film. I'm not saying that there isn't room for improvement. But I did find it enjoyable. As for what I would've done differently?
1) I would have made Pitssy, Ink, and Maginty more like their comic book versions. To be honest, I didn't even recognize the names as being from the comics when I saw the film. I didn't realize they were legitimate Punisher Comic characters until I read it on this thread. After going back and rereading those books, I deffinately agree that the characters should've been based on the comics in more than just name only.
2) I wouldn't have killed off Micro. I'd have kept him around for a possible sequal. Maybe have him design the Battle Van or something.
3) I would've made Jigsaw tougher. I'd also not kill him off, or at least not in such an obviously permanent fashion. In the comics, Jigsaw was always the one villain Frank could never quite kill. He messed up his face, shot him a number of times, beat him half to death, put him in intensive care, but never seems to be able to kill him.
4) Loony Bin Jim was a little too over the top. A characature of a psychotic killer. I would've made him more subtle, like the psychos the actor portrayed on CSI, Law + Order: SVU, Bait, etc. More Hannibal Lectar, less (Tim Burton's) Joker.
5) The FBI agent's wife and daughter could go. They could've been written better and had they been I would insist on keeping them. As it is I couldn't care less if they stayed or got cut.
6) The whole army recruitment with the American flag in the background was a little too cartoony. I'd have kept the montage, but cut the General Patton "homage".
Other than those few minor quibbles, I thought they did a fine job with the movie. I'm hoping they do a straight up sequel with the same guy playing Frank Castle, and maybe have The Punisher square off against Barracuda. I could totally see Michael Clark Duncan wearing the gold capped teeth with "F**k You" etched into them.