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>A box or a slot you can put pokemon in, on street passes it gets traded away with another person if he also has a pokemon in that slot.
>Actual IRL steps make eggs hatch, so if you walk around while you have eggs in your party they hatch
>A clock on any of the menus
>Communication doesn't end when you close the 3DS, or stays on for 5 minutes and then stops.
>Just fucking display the EVs instead of that hexagon, you can see them anyways if you use a reset bag and then reload.
>Display stats changes like +2 ATK -2 SPEED and debuffs like Leech Seed in battle, sometimes you just don't remember how many times the opponent used sand attack or you looked away for 5 seconds and missed what happened
>Being able to ride Pokemon who have the specific HM, which will be faster than bike.
>Getting a present on your birthday via wifi