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Pokemon incubator, you can put 6 eggs in a building and in 30 minutes they will hatch, you can come back and see the results. Sure is longer than going around in a bike but at least you cold do other game stuff like battling or catching while the eggs grow.
See this?, make so folder changes color according to the box wallpaper (or pokemon inside it)
Intro animations for Pokemon, just make them open their mouths when they enter battle at least, it feels so empty without them.
More utilities in towns so there's more reasons to go to them in the Post game.
Team photo like in HG/SS with the XY features (zoom, focus,etc)