Crawl through tall grass to avoid wild Pokemon
Trainers now become Alert (!) if they notice you and behind searching the area.
Finishing the game with zero alert phases and no pokekills nets you the Fennekin Hound award.
You're not really the MC, you're just a shlub who was brainwashed into thinking he's the MC because the real MC is too busy doing other things to be the MCof this game.
Team Rocket returns, Giovanni is now an elitist military leader seeker to create a one world government by putting the different regions against each other using an army of Genesects armed with nuclear weapons.
Bill is the new Otacon.
Professor Oaks lab is the new Outer Heaven.
Pokemon sent by the Oaker Heaven can be given different on base jobs carried by their skills and stats to generate income which can be used to upgrade tech like Pokeballs and Potions.
Speaking of which, trainers can be shaken down for items like Pokeballs and Potions.
Berries restore more health if properly cooked.
You can use the Xtranciever to call your mom for information regarding items and their effects.
The antagonist is some guy who lost to your dad's gym that thinks he's your brother because he's wearing his old running shoes.
Gary Oak was still here and Ash is still a loser.