Gold/Silver/Crystal/HG/SS
Ho-oh or Lugia?

Lugia.

Red/Blue/FR/LG
Mew or Mewtwo?

Mew.

Sapphire/Ruby/OR/AS
Groudon or Kyogre?

Kyogre.

Diamond/Pearl
Dialga or Palkia?

Dialga.

Black/White/B2/W2
Zekrom or Reshiram?

Zekrom.

X/Y
Xerneas or Yveltal?

Xerneas.