The introduction of Pokemon breeding + eggs + Steel Type + Dark Type.
Ruins of Alph
Non-gym leader Bosses (kimono girls, surfer girl squad, etc)
100+ more pokemon, plus the original 150.
Larger presence of Team Rocket
The introduction of the pokeRadio/phone/device?
The introduction of attachable items + more attributes
The introduction of Daytime/Nightime play + Weekday variables.
YOU CAN FIGHT 18 Gym leaders + The Elite Four + Red (the most powerful trainer you EVER meet in ANY of the pokemon games!)
And you can get Tyranitar. That guy was pure win, and you know it.
I put the STD in STUD, and all I need is U!