If they didn't want to make separate "fused" Pokemon they could just make "form" Pokemon that combine types, stats, and moves
Like the fusion would combine the primary types of the two Pokemon, so a Charizard fusing with a Swampert would be Fire/Water
Also, to allow every pokemon to fuse with every pokemon but not have to create a unique model for each, they could create what is essentially a pallette swap that reflects the type.
For example Charizard fusing with swampert would have a Blue Charizard with a steaming tail. This same model would be used for all Charizards fused with water types to save time and cart space but still allow everyone to fuse with everyone.
I still have no idea how to implement stats and moves tho