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Generation II

These are basically my theories on what changes might occur in the remakes of Gold and Silver. This does not include the usual things like improved music, new (animated) sprites, etc.

Gameplay

New movesets, especially for Chikorita. It's weak to the first 2 gyms' main types and Charmander, who's in the same situation, got Metal Claw for Brock, so why not?
PokéGear will be found on the touch screen after obtaining it. It'll look better of course, and it'll hopefully have new things with it, like the apps on the Pokétch.
Same rates (shiny, catch, etc.) as Diamond, Pearl and Platinum
Jasmine talking about her trip to/going to Sunyshore
New place for Rotom to transform. Maybe the Power Plant?
Obtain the Gracidea flower from somewhere by showing Shaymin (similar to Platinum). Maybe in Celadon City...
GS Ball Wi-fi event, similar to the Secret Key and the others.
Something for Deoxys's transformation, like the meteorites in Veilstone.
Global Terminal in Goldenrod City.
Gym Leaders can be fought again in their gyms or in a place like the Battleground.
Key items like the Vs. Seeker and Recorder are obtained.
Apricorns can be found in more places and maybe even planted like berries.
Balls made from them can't be traded to DPPt.
New balls from Gen III and DPPt can be found.
Pokémon caught in Johto will either show that they're from Johto or Faraway Place when traded to DPPt.
Safari Zone is open.
Red is still fought but the levels of his Pokémon are changed to be somewhat more similar to Pearl's Pokémon's final levels.
Some items, like the Berserk Gene, are removed while ones new from RSEFRLGDPPt are added.
Rules of Battle Tower are similar to the one in Sinnoh.
Pokémon from Kanto, Hoenn and Sinnoh can be found in the wild after the Elite Four.
Pokémon Contests are added. Poffins too?
The stone Oak mentions in the in-game Shaymin event can be found in Kanto somewhere.
Certain areas have weather, like hail outside the Ice Pass.
Some trainers are relocated so Double Battles can be initiated.
The new berries in Gen. III and DPPt are found in many locations.
New locations after going through Kanto maybe, like the Sevii Islands in FRLG.
NPCs talk about Sinnoh and even the Legendary birds going there. Talk about Hoenn too.
More Pokémon in the Johto Dex, like the evolutions Gliscor and Yanmega, following Platinum's example.
An underground like the one in Sinnoh?
Pal Park?
Wind which affects certain aspects like:
- Speed in battle, like the move Tailwind
  - Headwind effect on certain occasions
- Drifloon's coming (Gligar too?)
- Suicune's location; it goes with the north wind
New look for Shellos, Gastrodon and Mantyke
Coronet/Moss/Ice Stone, like in MD, for the location evolution
- Use it like other stones or hold it and level up
The Kimono Sisters get two new younger twin sisters who have Leafeon and Glaceon.
Mewtwo can be caught on New Island.

Story

More involvement of Ho-Oh/Lugia in the story. They're the mascots.
Ho-Oh can't be caught in the Silver remake. Same for Lugia in the Gold remake.
Eusine appears and is involved in the story, maybe like Lance and Cynthia.
More active Gym Leaders, like Wake and Maylene in Platinum.
A story-related double battle with an character in the game, like the one with Pearl on Spear Pillar.
Rocket's current leader has a name and a different sprite.

Trainers

These are my predictions for certain trainers. I won't bother list levels. I'll just say that I think they'll be a bit similar to DPPt. The first line is their party during the first fight and the one under it is for when they're battled again. It may get repetitive...