Minecraft has come a long way since Classic, and I think there's still a ton of things that could be added to make the game better.
More varied sky colors. Minecraft isn't supposed to be realistic, but it could use a bit more variation in some areas. For example there could be different sky colors depending on biome, like a orangy color sky for a mesa or a dusty color for a desert.
More mobs. Minecraft definitely does not seem very alive, so why not add more mobs? Some don't have to drop anything and can be there just for effect (like bats)
More food. Some cocoa beans, milk and sugar on the crafting grid could give you milk chocolate (always yummy) and a loaf of bread could be made into 8 slices of bread, and you could use any kind of meat to make a sandwich.
Different types of villages + villages in different dimensions. Doesn't seem to be much village variation besides size, so why not have different types of villages depending on what kind of biome they spawn in? (hot/cold/medium temperature)
More varied terrain generation. Even though the 1.7.2 biomes update really diversified the terrain, I feel that there could be higher mountains, deeper and wider caves and ravines, and valleys that go down below sea level, and maybe even new biomes with their own defining characteristics.
Different types of caves. I feel exploring needs to be a bit more exciting, so I feel that there should be more types of caves, maybe crystal caves like the ones seen in real life?
More sound. Birds chirping when you're in a forest biome, dust blowing in a desert/mesa, etc.
More generated structures. I feel that Minecraft is sort of lacking randomly generated sturctures, and that these things could be more exciting to explore, like the dungeons. They are really small and it takes you like 15-60 seconds to raid one.
More methods of transportation. If it's possible, add giant tameable, ridable birds.
Toilets. If you watch ExplodingTNT's videos on YouTube, you'll get the reference I just made here.
