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Probably age. For legendary or rare pokemon like dragonite, it's possible that they are able to live for aeons. Such pokemon, when raised from a young age by trainers, would be at their minimum potential size following evolution. However, because they contain boundless amounts of energy, they continually grow. This might not be so obvious to a trainer, since their lifespan pales in comparison to the length of time a dragonite has to live and grow. That particular dragonite from the anime had been wandering the seas for years, maybe even centuries, so it could have been continually growing larger that entire time. It's also possible that it was abnormally large to start with, being the initial cause of its loneliness in setting it apart from others from its kind.
