If I could make mods....
• Zombies would spawn in places without roofs and away from players so they don't spawn inside your castle.
• They spawn far away, that way they have to travel to reach you. (Could take up to 2 minutes for the first wave to reach you, and it's cool to wait to see the hordes in the distance, or perhaps they spawn at sunrise and it takes a whole day for them to reach you)
• Give zombies the ability to think of the best way of breaking in and/or climbing over.
• Different types, zombies that are ground, others that are pirate zombies that travel over water, creepers(rare) that blow up, flying zombie birds(archers would be important)
• Depending on height, zombie birds would be more prolific.
• Zombies would drop realistic goods, armor, weapons, building blocks, food, seeds...
• Plants would sometimes randomly sprout throughout the world.
• Sea tide would rise at night, lower in morning and large bodies of water vary in quantity over time.
• Zombies could spawn from dirt/sand/soft ground material. As if coming from the grave
• Difficulty would increase depending on how long the players are surviving and how large their fort is.
• Villagers would be smart enough to defend themselves against zombies, joining a town would give you good starting resource and the villager guards would help defend. Also the town's iron golems.
Essentially the mod would be everything consisting of trying to create a sustainable safe habitat in an apocalyptic world.
Everything Minecraft should have been.
Edit: It'd be cool to see how long an intelligent village could last granted they could collect resources, defend, build using a structure algorithm and even mine to build themselves better equipment.