I'd say the egg system is the best thing they've included since the original versions.
Gold/Silver: Egg system. And the Dark/Steel types.
Ruby/Sapphire: Pok
GSC: Hold items
RSE: Traits and abilities
DP: Online, phys/spec split
G/S/C: Backpack pocket system and holding items/mail
R/S/E: Pokemon abilities
D/S: Pokeapps, wifi, physical/special split. Now I don't have to memorize which ones do which.
GSC: Hold items
RSE: Natures
DP: Physical/Special split
Breeding, abilities, move split.
Morning, Day, Night and Midnight shifts.
GSC: Hold Items
RSE: Double Battles
DP: Pokemon Eggs hatching at Lv.1
[COLOR="DarkOrange"]Breeding System... Pokemon Abilities and Double Battling.... and then the GTS.
Oh, how I love the GTS.[/COLOR]