1. Day/Night
2. Berry Trees
3. All of the first 251 Pokémon in the Regional Dex, plus their evos and babies from Gens 3, 4, and 6
4. Pokémon Amie
5. GB Sounds available near start of game
6. Moss Rock added to Viridian Forest and Ice Rock added to Seafoam Islands (for Leafeon and Glaceon)
7. New electromagnetic area added near Power Plant (for Magnezone)
8. Starter Pikachu gets a Light Ball around Cerulean or Vermillion (around the time it started to become obsolete in the original)
9. Rival's Eevee can now evolve into either Espeon, Umbreon, or Leafeon in addition to the original three Eeveelutions (couldn't think of a way to fit either Glaceon or Sylveon onto his team)
10. Jessie and James are a double battle and have more appearances after Silph Co.
11. Level curve is the same as Yellow, but with two major exceptions--Koga's ace is now Level 42, and Sabrina's is Level 45 (they were both Level 50 in the original, way too high for that point of the game)
12. Pikachu can now learn Surf straight from the HM
13. The VS Seeker from FRLG returns
14. The Fame Checker from FRLG also returns, but now has a reward for completing it
15. The gift Kanto Starters are all holding Mega Stones
16. The Sevii Islands return, but are expanded and fleshed out into a real region (the extra islands that were cut from FRLG would also be included)
17. The encounter with Lorelei in Icefall Cave would be a tag battle against Petrel and Proton
18. Prof. Rowan shows up in the postgame and gives you a Sinnoh Starter
19. Gym Leader and Elite Four rematches (they'll all have Megas on their rematch teams)
20. All Elite Four members appear in the postgame on certain days of the week in a Double Battle:
- Bruno and Brawly at Mt. Ember
- Agatha and either Prof. Oak or Bertha at Pokémon Tower
- Lorelei and Lance at Navel Rock (couldn't think of any other friend for Lorelei, and HGSS already did Lance and Clair; plus, I really ship Lance/Lorelei)
21. Eusine appears in Celadon City, and after you speak to him, the Legendary Dogs will start roaming Kanto
22. The following later Gen characters all have cameos: Silver, Janine, Clair, Karen, maybe Alder or Diantha (I'm not a fan of Cynthia, and she's appeared in way too many games, IMO)
23. Lugia and Ho-Oh return to Navel Rock, but are no longer event-exclusive
24. Lugia's connection to Articuno, Zapdos, and Moltres is fleshed-out
25. Mewtwo's backstory is fleshed-out
26. Either Dialga/Palkia/Giratina or Reshiram/Zekrom/Kyurem are all catchable in a postgame area (just like Groudon/Kyogre/Rayquaza in HGSS)
27. The (lame) Battle Tower near Seven Island is replaced with the Hoenn Battle Frontier (just like HGSS had the Sinnoh Battle Frontier)
28. Unselected player character appears as a secondary rival with Clefairy as their starter (like Ethan/Lyra in HGSS)
29. The following get Megas (among others)--Raichu (Electric/Fairy), the Nidoroyals (Poison/Ground), Clefable (Fairy), Vileplume (Grass/Poison), Ninetales (Fire/Ghost), Arcanine (Fire/Dragon), Machamp (Fighting), Victreebel (Grass/Poison), Golem (Rock/Ground), Rapidash (Fire/Flying), Exeggutor (Grass), Starmie (Water/Psychic), Mr. Mime (Psychic/Fairy), Jynx (Ice/Fairy), Tauros (Normal), Lapras (Water), Omastar (Rock/Water), Kabutops (Rock/Water), Dragonite (Dragon/Fairy), Crobat (Poison/Flying), Bellossom (Grass/Fairy), Azumarill (Water/Fairy), Quagsire (Water/Ground), Slowking (Water/Psychic), Miltank (Normal), Ambipom (Normal/Fighting), Mismagius (Ghost/Fairy), Weavile (Dark/Ice), Rhyperior (Ground/Rock), Togekiss (Fairy/Flying), Yanmega (Bug/Dragon), and Mamoswine (Ground/Ice)
As for the Rival's Eevee...
1. Eevee => Vaporeon (replaces Cloyster): Lose to him in Oak's Lab
2. Eevee => Jolteon (replaces Magnezone): After beating him in Oak's lab, defeat his Eevee on Route 22 with a Special attack
3. Eevee => Flareon (replaces Ninetales): After beating him in Oak's lab, either skip or lose the battle on Route 22 during the day
4. Eevee => Espeon (replaces Alakazam): After beating him in Oak's lab, either skip or lose the battle on Route 22 during the morning
5. Eevee => Umbreon (replaces Tyranitar): After beating him in Oak's lab, either skip or lose the battle on Route 22 during the night
6. Eevee => Leafeon (replaces Exeggutor): After beating him in Oak's lab, defeat his Eevee on Route 22 with a Physical attack