Unown ! and Unown ? were both created in Ruby and Sapphire, though they weren't accessible until FireRed and LeafGreen.
Deoxys' Attack Forme was made for FireRed and its Defense Forme was made for LeafGreen. Its Speed Forme was made for Emerald.
Giratina got its Origin Forme in Platinum, and its original form was retroactively named its Altered Form.
Shaymin got its Sky Forme in Platinum, and its original form was retroactively named its Land Forme.
Rotom got Heat Rotom, Wash Rotom, Frost Rotom, Fan Rotom, and Mow Rotom in Platinum.
Kyurem got Black Kyurem and White Kyurem in B2W2.
Keldeo got its Resolute Form in B2W2, and its original form was retroactively called its Ordinary Form.
Zygarde got its 10% Forme and Complete Forme in Sun and Moon, though they first appeared in the anime, and its original form was retroactively called its 50% Forme. 10% Forme with Aura Breaker and 10% Forme with Power Construct are also considered separate Pokémon internally, as are its 50% Formes with Aura Breaker and Power Construct.
Hoopa Unbound was introduced in ORAS and the original Hoopa was retroactively called Hoopa Confined.
Ash-Greninja debuted in the anime, but its first mainline game was Sun and Moon. Battle Bond Greninja is also considered separate internally to a Greninja with Torrent or Protean.
We can also look at Mega Evolutions introduced in ORAS or maybe even Primal Reversions.
