I really liked Silver/Crystal.
1. You were able to go to 2 regions and collect 16 gym badges.
2. This was the first time you could breed pokemon. And you were able to have rematches with trainers.
3. The pokemon in that game were AWESOME!
I did have Ruby and Sapphire.
It was a disappointment they didn't keep the Following pokemon...
Evee, which had 5 Evolutions.
Larvatar, which evolved into the good Tyranitar.
Houndoom, which was a fire/dark type. Would have been the better alternative than Mightyena. Mightyena was not that great for a dark type. Pretty crappy, actually.
I can't think of any others right now.