Full disclosure: I loved Merle and Dwight's storyline so I'm not saying this would be better than what we got. Just a what if scenario.
Season 1: Rick goes back to rescue Merle like usual, everything remains the same except one thing. After they dealt with the Vatos scenario, Daryl tells Rick he's not coming back with them. There's nobody back at the camp for him and Merle is still out there. He takes his leave and that's the last we see of him. Morales, meanwhile, stays with Rick's group.
The night Amy dies is remixed. The cold opening shows the camp being ambushed by walkers, seemingly well coordinated out of nowhere. Everyone who survived before still survives except a few people, Morales' wife and kids.
In the aftermath, the group comes to the conclusion that they were just unlucky and that the Walkers happened upon them. Morales mourns but moves on before Season 2 ends. He takes Daryl's role as Rick's righthand man and Carol's BFF (since they can bond over their dead family.) A big reason for this is so we don't have MORE characters coincidentally running into Rick hundreds of miles away over a year later.
The storylines remains more or less the same from the farm to the first attack on the Savior's satellite outpost. Big difference is that there is no Dwight. It's Daryl