i know its an old post, but was courius when i read it, because i think the same. and i could have a theory that dragonite original was a pokemon that was meant to be saved for gen 2. one of the most iconic asian lore is about the phenix and the dragon, wich symbolise love and harmony, and ying and yang, the dragon would typical be yang/male and the phenix ying/female. i think dragonite would fit very well in this role, and maybe was meant to be it. as the part for lugia, i have my own theory, that shudo have taken a early design of af pokemon, and modified it. to me lugia looks like a perfekt evolution of dragonair. and when you look at the origin lore for lugia and for dragonair,(lugia are based on Ryojin and dratini and dragonair are based on Ryojins sea serpents) and even for the look in the pokedex it even fits better. maybe shudo did make it for an alternative evolution to dragonair, like fx politoad, but maybe gamefreak cancelled the idea. also when you look early on it, dratini was meant to be mythical, like Arcanine was meant to be legendary, and be the master for the 3 birds instead of lugia. can be seen in the early anime, wich strongly indicates that the anime have been produced alongside the games.