Make biomes move, grow, and change, like in real life. Systemic mechanics such as biomes that change naturally would give rise to different gameplay options and situations that would not be easily codable without them.
For example, having a plains biome turn into a forest biome when enough trees are detected in an area, and having it turn back into a plains biome when not enough trees are detected. Having forests grow and spread would also be a mechanic to be added.
Another example would be plains turning into a desert biome when not enough rainfall happens, or not enough water is in an area, and having it turn back when enough water is present.
There are many more good ideas, these are just a couple of examples.
To do this, we can use the rainfall amount generated per biome. However, we need to make rainfall independant of biomes, and instead have rainfall cause biomes to spread, as opposed to what the game does currently.
First, when we start a new world, the game generates the terrain.
Then depending on the terrain generated, a first rainfall map would be generated. For example, terrain near bodies of water would have more rainfall.
Finally, we make this rainfall map fluctuate depending on the terrain. Terrain near water has more rainfall, and therefore, grows vegetation. Terrain farther from water or in a rainshadow gets less rainfall, and therefore, grows less vegetation. So much more can be done with this.
Mechanics like these would give rise to new and interesting situations, and breath new life into the game, without adding new blocks or items. This would make minecraft feel like a living, breathing world!