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The only thing I can think of that would make sense and fit in is...
Cosmic type (or Alien/Space/Unknown)
Aliens and pokémon from other worlds and dimensions that are not native to this planet belong to this type.
Solrock and Lunatone are now Rock/Cosmic
Staryu/Starmie are now Water/Cosmic
Elgyem/Beheeyem are Psychic/Cosmic
Clefairy line are now Fairy/Cosmic
Unknown are now pure Cosmic
Deoxys is now pure Cosmic
The new legendary is based on Cthulhu and is a water/cosmic or dragon/cosmic deepsea monster who awakens from his slumber in the depths and must be stopped by the player. As the story progresses the effects of his arrival can be seen in the people you meet who gradually become more and more twisted. The villainous team are a cult of his followers who aim to bring about the end. Your rival starts as a close friend but gradually falls victim to the whispers from the deep. You and the regional champion must defeat the looming threat with your pokébros and save the rival and the pokémon world in the final battle. Arceus appears and fights with you as this creature is not a part of his design but a an ancient traveller from another universe.
Moves for my new type could be things like:
Plasma Blast (special, chance to burn)
Starlight (heals a random member of party)
not-so-draco Meteor (physical, arrives after 2 turns for massive damage)
Phase Out (you are damage immune next turn)
New pokémon that would be Cosmic type would include a Steel/Cosmic Saucer that's rumored to "beam people up", but actually is kind and only trying to help those in danger. There could also be a Dark/Cosmic goblin pokémon who steals things by walking through portals it creates.
The Cosmic gym leader is a retired astronaut or an astrophycisist and his/her gym a research station with a giant dish on top. To progress you have to navigate through a zero-gravity chamber.
So what do you think, is it stupid? I'm a writer so I tend to go overboard when I have an idea...