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I've had an idea for PokemonxMonsters for a while.
>DQ Breeding system: skills are passed on from parent to child, could also be useful for implementing hidden abilities in here. So Breeding a speed boost Blaziken, for example, would be less time consuming and potentially more rewarding. Only Pokémon that were bred through certain combinations can Mega Evolve.
>Stats are now edited on either side to be closer to the others: either Pokémon are buffed (initially) or monsters are nerfed
>Monsters and Pokémon have both types and families
>a few new creatures that are essentially just fusions
>Mega Evolution is expanded into a high tension skillset, certain monsters such as: Incarnus, Rhapthorne, and Psaro have this skill along with all Pokémon that mega Evolve
>Take a few hundred creatures from each (no recolors for monsters, pick and choose from Pokémon)
>Arceus, Giratina and TimespaceDuo are Incarni, Zygarde is Slime, Hoopa is Demon, etc.