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Certain Pokemon will only be available at night. Time will change in real-time, so when it's night for you, it's night in the game.
You can get more than one masterball.
You don't even need to worry about switching boxes anymore.
Pokemon will have effects that work similar to moves, but activate automatically. Spiky Pokemon, for example, may hurt Pokemon that use attacks that would make contact.
Ash will never age, but Misty, Brock, and Gary will, and Misty and Brock will stop traveling with him.
There's going to be a time travel plant legendary, a shooting star metal legendary, and an alien legendary.
The person who voices Meowth in the anime is going to die before the 5th generation of games, but not before voicing a killer robot in the Sonic the Hedgehog series.
There are Pokemon that can fight on equal footing against Mewtwo that aren't Mewtwo.
Eevee will have a grass type evolution. It will not use the Leaf Stone.
I think I just won.