Personally, I would like to see:
-the fish model that Notch couldn't originally implement due to time constraints
-some use for emeralds besides trading with the Squidwards
-something similar to the Physics Craft mod, with ropes and such
-change of bread crafting: Instead of just plonking three bushels of wheat into a crafting table, you would have to put the wheat into a crafting table(just one piece of wheat, placed anywhere) to make flour, then cooking the flour in a furnace would make bread
-as long as Mojang continues to add potions, they might as well add potions of flight into the game
-Adding above ground strongholds, as it never made sense to me that they were so far underground
-Sea life(coral, fish, etc.) would be nice, as it would give more life to the game.