Could well be, but he might have made a bigger problem for himself as when would have added a friend path instead. I do not know his plans though, but guess in my opinion it could have been wiser if he first had developed other girls more and untangled them a bit from Nea if this was his plan. If he intends Nea to be close to family he has a problem anyway now, with very different branches.
Personally I do not dislike Nea, but did think that she feels too much as the main girl with to fast development compared to others, while there are others that have hardly had any real progress and story almost still has to start like Mom, Tess (that pool party still has to happen that was foreshadowed long ago
) , Heather, Yui and a few others. Will be harder now since their setup is still and feels at start and not even there really and they need work to setup while the one developed char is either gone and that should have quite an impact on MC and not a great one with at least some guilt quite natural or close to sex stage with her.