Okami: The rejuvenations are no longer persistent, and regions become corrupted again the moment you leave them.
Mario Kart 8: You have a fuel gauge, and need to refuel after every other lap at the start. Using boosts consumes more fuel.
Bayonetta: The designs models of Enzo and Rodin are now swapped.
Chrono Trigger: Magus' default name is now "Wally". You can still change it freely, but this is what he'll be referred as in all the wikis and forum discussions.
Castlevania: Aria of Sorrow: Since Soma inherited Dracula's power, he can no longer regain health from food items. His only other option is to consume the few human NPCs in the game, or find someone in the prisons.
The Legend of Zelda: Link's Awakening: A snoring sound effect now permeates the entire game's soundscape.
Resident Evil 4: The mysterious merchant reveals his identity to be Leon's estranged father.
Paper Mario: After each chapter, you're forced to go back to your house to cook dinner for Luigi, because he's afraid to use the stove.
Mega Man 2: Mega Man now screams "YEAH" every time he jumps.
Undertale: Achievements for both the "pacifist" and "genocide" endings.
Ocarina of Time: Banjo Kazooie-style voices for the dialogue.
Remove wild Pokemon catching, instead there's a gacha system where you have to buy Pokeballs containing random Pokemon
You just made me stare into the alternate reality where Pokémon was first created for mobile, rather than the original Gameboy.