Mewtwo. It may already have one, but I don't like it.
But. Gen 1: the legendary birds Gen 2: the legendary birds Gen 3: Rayquaza or Salamence. Don't see Metagross working. Gen 4: Arceus. Obviously. Or Dialga and Palkia. Or Garchomp. Gen 5: White/Black Kyurem. If that's even possible. If not, Hydreigon. Gen 6 (so far): Yveltal.