I want to see various resources that only show up in certain parts of the world. Special dyes, extra-strong ores, gemstones, different kinds of flowers/mushrooms... just anything to differentiate areas. Let this go beyond even biomes, and thereby establish a reason for trading and conquest in multiplayer.
Alternately/additionally, let players learn advanced crafting techniques. Things like Damascus Steel production, or fancy stonework, or wood carving. Let one player learn how to make picks with double the normal cutting speed, or doubled durability, and Minecraft's multiplayer will increase greatly in depth.