The best replacement for rayquaza is deoxys.

The best alternatives to rayquaza are rated as following:
★★★★★  deoxys
★★★★  groudon
★★★★  lugia
★★★★  giratina
★★★  mewtwo
★★  dragonite
★★  kyogre
★★  salamence
★★  arceus
★  dialga
★  latios
★  deoxys movie
★  darkrai
★  celebi
★  palkia
★  yveltal
★  zekrom
★  reshiram
  latias
  deoxy
  kyurem
  deoxys video
  mew

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Google Trends

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rayquaza
deoxys
groudon