Two regions is the best part for me. They introduced a lot of my favorite Pokemon. The starters might not be great competitive pokemon but they all have great designs. The legends look excellent as well. I also think that the elite four is really difficult and I think that's a really good thing. I've played Gold and Silver and Heart Gold and Soul Silver so much and I still have trouble sometimes. Also Red is really epic. Is there anything else like that in other games? Finding him and seeing a level 81 Pokemon for the first time that belonged to a character in the game was actually really incredible for me as a youngster.
As far as things that were introduced there are a ton.
A Pokemon being able to hold an item.
Breeding
Dark and Steel types.
Shinies
Pokemon genders.
Moves like Protect, Outrage, Megahorn, Pain Split, Spikes, Extreme Speed, Mega Drain and Sunny Day.
The first time you could play as a girl.
Friendship
SPECIAL stat was split to Special Attack and Special Defense.