Well, a great plot for 'Walking Dead Do Over' fanfiction might be to explore what would happen if the group had found a more secure location right from the start. Say they stumbled upon an abandoned military base that was still stocked with supplies and weapons. This would change the entire dynamic as they wouldn't be constantly on the run for resources. Also, a plot where a character has premonitions in their dreams about future zombie attacks and they use this knowledge to prepare the group better. It could add a supernatural element to the otherwise gritty survival story.
Definitely Carl. In a 'Walking Dead Do Over' fanfiction, you could show his growth in a different way. Since he was a kid in the original, here you could have him be more involved in decision - making from an earlier age. Glenn could also be interesting. You could rewrite his story to make him even more of a hero, like having him come up with brilliant strategies for scavenging and survival. And then there's Negan. You could explore his character in a different light, perhaps showing a more redeemable side of him if things had been different in the story.
Yes, the The walking Dead comic series has ended. The creators decided it was time to bring the story to a close and leave a lasting impression on fans.