I played with this idea in a comment on a meme in the gaming stream, but what if there used to be multiple Legendary Pokemon? It would certainly explain why Walking Wake, a primal version of Suicune exists. However before Suicune Raikou and Entei became what they are today, they died in a fire and were brought back to life by Ho-Oh. Could Walking Wake be the original form of Suicune before dying, or just an ancestor. And what about the "future" versions of Pokemon? Why are all the Pokemon in the future robots? And why does Cyclizar look so lame in the modern day, when its ancestors and descendants look incredible? There are too many questions and not enough answers about the Pokemon series.