Who would Ryudo choose: Elena or Millenia?

I think Ryudo would pick both. As they are actually the same person, it's not completely wrong - Ryudo is in love with one unique soul, after all. Elena and Millenia are like the two sides of a single coin.

I think that's what Game Arts wanted to show, but they couldn't, because the game would be very controversial and misunderstood by the church and governments.

In the game, Ryudo says he can't choose between the two, and that he loves both. Elena says the three have a special bound. And Millenia says she learnt to share her heart with Ryudo and Elena. So I think that's it, the three will be together.

Besides, Game Arts wanted a 100% happy ending. Would it be happy if Ryudo did choose one? The other would have her heart broken. And, as Ryudo showed love for both (and the girls for Ryudo) during the game, it would be dull not to end with some romance.