Had an idea for Tornadus, Thundurus and Landorus where a very long time ago the three were like siblings where they would fight each other but not with hate. All three had a crush on Enamorus and wanted to be with her. She had told them to show her their best to be with her BUT they thought that meant that the one who can beat the others can be with her so they fought more and more until they forgot about their crush on Enamorus and why they are even fighting each other so much in the first place. Enamorus still remembers how they mistook her words and when she joins would explain this to the MC. Might need all three of them to get to her.
I could also see Mewtwo getting along with Yveltal since both had felt they should not be loved and had been seen as a weapon so they both kinda understand each other in a way.
Also could Xerneas personality be a little unpredictable. My reason for this is since she represents life and real life is unpredictable at any time with good and bad happening. An example would be one day she would be cuddly and the next she wants to feel the MC under her ass pounding away on him without holding anything back even if it hurts it wont leave damage due to her ability. The one thing that would remain constant would be her absolute love for pregnancies and big belly's and milk heavy tits.