Although not specifically directed towards you, your comments have many points that hold relevance to my own thoughts.
While I don't have a 3d relationship myself, I don't think you should be so quick to condemn those who have both a 3d relationship and a waifu. Truth be told, you are projecting your idea of love and a "proper" relationship on this person, even though you have no grounds to do so. Could you disagree? Of course. But you can't call him "wrong" for it, because it's relative to the individual.
Consider it like this. Waifus mean different things for different people. For some, it is their favourite character. For others, it's an inspiration they look up to and deem perfect, someone that they may feel unworthy of yet worship. For many, it lies somewhere in between, standing parallol to the concept of a "god" as people usually understand the idea. A benevolent being that watches over the person, guiding and inspiring them. I believe it's as possible to have both a relationship with a 3d and a waifu, as one would with a 3d and god. In that case, there is a different aspect of love, and a reconciliation between the two that must be made. One must be made aware of the other, and the person come to terms who they value more: their waifu or their 3d partner. But it is certainly a possibility.
Do I feel it is appropriate for my relationship with my own beloved? No. But I would not call someone out on it, as much as I would someone who is gay or likes someone of a different race. It matters not to me. Nor should it to you either. It affects you how, exactly?
I personally feel it's akin to a religious experience, and waifuism in some shape or form will grow increasingly popular as time goes on. People have always had a need for spiritual fulfillment and a desire to worship or believe in ideals. In the past, it was through organized religion; today, it is increasingly personal, depending on the individual to find their own god, their inspiration in life to follow.
I wouldn't trouble myself with such things, truth be told. Live, and let live, as the saying goes? Just embrace the waifu in your heart and believe in the power of love that will conquer evil and darkness.