For this idea I want to be absolutely clear that this is all consensual with all legends being of sound mind and body with absolutely no outside influence having influenced or forced the female legend to do this of any kind. This is done entirely of her own free will and does understand this.
The idea that I had come up with is that by the end of the game the MC will have 1,000 or more children with the legendary Pokémon and I am not talking about the children with humans (they are NOT part of this in any way) with this idea only the legendary Pokémon are used. So there is a very tiny (none zero) chance one of the children (female) are born a little different than the rest. She would be born with an attraction to the MC (her father). She does understand that this is not entirely normal and does not pursue this, thinking it will pass but it does not. She talks with Maple (Maple would have made a Pokémon translator by this time) and then tells her own mother that she wants to be in the same relationship to the MC. The daughter does not only work to get the OK from her mother but also every sing member of the harem of the MC so that everyone is ok with this. If any member was not ok with it she would stop and not want to disrupt what is there. She gets the ok from ALL members that is not the MC before revealing and asking the MC if he is ok being in a sexual relationship with his daughter. This would be a choice of the player "YES" or "NO" with absolutely no consequences if rejected. If the player chooses , NO, then she will respect the MC's wishes and end it there. If YES then she would then be a relation ship with him ONLY because EVERYONE was fine with it. The MC has had NO contact with her or has influenced her in any way to get her to be this way. This is done ENTIRLY of her own free will and understands what this involves and what will happen.
This does not change the MC in any way and he will continue to to have parent and child relationship with his other children and does not even think to try and change that from his side in any way.
I now say that the daughter was BORN this way and nothing and no one has influenced her choices in the slightest and she wants to make sure that every single person of the harem knows about this and gets there ok before telling and asking the MC.