If I could start the franchise over to where we never had a Punisher movie, I'd like to do it in three movies spanning decades.
The first is in the 70's right after his tour of duty. This is where we get to see his training and his psyche during the Vietnam war. The losing of his family driving him over the edge. The punishment he dishes out and his starting his one man war.
The 2nd one takes place in the late 80's and he's somewhat of an urban legend, but the Police, Feds and of course the mob know he is real. During the movie he's caught on camera and shown to the world that there is indeed a Punisher. He's captured by the police and put on trial. He's put in Rykers and such.
The 3rd one is mid 2000's. He's been fighting this war for over 30's, he's beaten and scarred heavily. This is the one where you go balls to the wall with everything. The first two movies led up to this.
As far as a story for each, I obviously don't have any ideas. Just certain scenes I have in my head or certain issues to develop like Hensleigh did with the 2004 Punisher.