-New clothes for the main characters. After reading all of Pokémon Special manga, I'm tired of seeing Gold in those clothes.
-Obviously, playing as a female (Crystal)
-Possibly a chance at playing as Silver instead of Gold (I dunno. Each game aside from RS, I've always wanted to play as the rival i.e. Blue, Silver, Barry)
-A more in-depth look at Silver's history instead of just being a mean thief who stole a starter Pokémon and only likes "strong" Pokémon
-Definitely the Togepi egg. I always used it on my Pokémon team.
-The Odd Egg at the Daycare center. The idea of having a Pokémon that won't be available 'til much later on in the game is very appealing.
-The PokéGear with calling, radio, and clock features. Possibly more added would be amazing
-Maybe some Gym Leaders a bit more difficult with higher leveled Pokémon
-The Bug Catching Contest
-The old Berry system. The newer berries (Sitrus, Oran, Nanab, etc.) can be found on dark spots on the ground like in FRLG.
-Apricots to get free Pokéballs from Kurt
-MysteryGift the way it used to be where we can get furniture and items for our houses
-Mom money saving feature
-Getting to capture both Ho-oh and Lugia
-Suicune, Raikou, and Entei roaming Johto
-Celebi event some time after the release of HGSS through MysteryGift, giving the player Celebi itself, or the GS Ball
-The Grooming Brothers and Daisy so it's easier to raise Pokémon Happiness.
-Swarms. I don't remember how prominent of a feature this was back in the day. I do however remember getting calls from trainers saying that Pokémon like Marill and Quilfish were being found in abundance.
-The siblings who give away type boosting items.
-The Dragon Den with the possibility of getting a Extremespeed Dratini.
-Re-battling gym leaders.
-More difficult Elite 4 - both in Johto and Kanto.
-More in-depth on the storyline with Team Rocket
-SAFARI ZONE IN FUCHSIA CITY - Very important since the one that was supposed to be in GSC never made it
-More Pokémon around Mt. Silver
-VS. Seeker
-Battle Tower from Crystal. Maybe more expanded?
And that's all that I can think of on the top of my head.