Not sure if someone already suggested something similar, but I had a funny for Xerneas when it's time.
Idea is if you need to fight other Pokemon who don't want you breeding with her. Logic is that wild Pokemon know about the MC now, and are afraid of Xerneas and her breeding kink even before. Could even make it so the enemy Pokemon are dragons and get some opportunities to tie into Zygarde's interventions.
Edit: realized that an alternative if this is strange would be Xerneas making you answer questions about breeding to figure out whether she'll go with the MC or if she'll try to demand he stay with her. Too many good options with her.