Fusions are thing that everyone loves to imagine and want in a game and they could be incorporated into the game by the Cult of Perfection in their quest to find the perfect being.
Ideas with Examples:
1.only a certain few pokemon can fuse because of DNA or something so that their is not an insane amount of fusions
EX: a Ninetails can fuse with a Luxray but cant fuse with a with a Absol despite Absol being able to fuse with Luxray as well
- only Deltas can fuse because they all have a common gene and screwed up DNA
EX: Delta Charizard can fuse with Delta Gallade after obtaining XX thing
- Perfection Cult fails in getting the Original Dragon but learns about how to fuse certain pokemon through experiments but are only able to take bits and pieces of certain pokemon and only certain pokemon can be the base and others can be replacements and only chhanging certain stats
EX: A Machamp can be a base and gain the Legs of a Lucario and increase it speed stat but lucario can only do this with Machamp and nothing else