The best replacement for flygon is salamence.

The best alternatives to flygon are rated as following:
★★★★★  salamence
★★★★★  altaria
★★★★★  garchomp
★★★  dragonite
★★★  tyranitar
★★  claydol
★★  archeops
★  skarmory
★  crobat
★  kingdra
★  gliscor
★  goodra
★  haxorus
★  salamence emerald
★  krookodile
★  noivern
  aerodactyl
  tyrantrum
  aggron

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flygon
salamence
altaria