I could see Eternatus later being in a non hostile freindship with rayquaza and zygarde. Reason: eternatus can absorb energy which would make them initialy hate her but they could find out that her ability can help lessen there burden of mitigating the fight between kyogre/ groudon and xerneas/yveltal. Her ability would be able to dreasticaly reduce the effects of the battles to the surounding area thus there is less mess to clean up.
If zygarde does showdown in the town near the boat to get the MC this could be good to do officer Jenny since the MC would have protected the town and quelling the disruption thus she could be thankful for reducing the amount of paperwork when the legendries protected the surroundings if no other girl is available.
Could there be an option where the pokemon who are heavely pregnant get cravings EX: Moltres hot-pot, articuno ice cream.