When I saw that no one has made a hierarchy of pokemon I decided to make one my self. Here it is in all its MS Paint glory.
I didn't include The Birds The Dogs The Regis The Lake Trio Ho-oh Lugia or Jirachi because I didn't know where they fit in.
Comments or feedback appreciated.
Edit: The reason Clefairy is with Palkia and Deoxys is beacause Clefairy was shown in the Kanto anime episode " Clefairy and the Moon Stone" to be from outer space
UPDATE: I have taken all of your advice and updated The Hierarchy here is the new version with The Birds The Dogs The Regis and The Lake Trio. I have also made it neater and easier to read.