Have you ever considered the fact that new characters with completely new movesets take a lot of time and resources? Clones are way easier to make, and besides, clones don't take new character slots, they're just there because Sakurai and his team had some extra time to create them.

People still fail to understand that clones like Dark pit were thrown in last minute of development as a bonus to help pad out the roster, little effort is needed to create their design and change the properties of their attacks. Because they require little effort trading one clone for a unique character wouldn't be a equivalent exchange, you would at least need 4-6 clones to accumulate enough development time for one unique character.

Basically the reason why didn't get unique character is because of time constraints, not because a clone stole it's spot to be in the roster.

P.S. Personally I would rather have Hades over Medusa.