Basic Bakura is more prevalent overall than basic Marik. He has been around longer, and he has been a supporting character. I see Bakura as being more likely to be added.
I really hate to say it, but Konami does seem to be pretending that poor Ryou doesn't even exist. Are they hardcore fans of the abridged series or something? Since we now have the non-yami Yugi, and probably the same for Marik in the future, then why not Ryou as well?
True. But I figured Konami could make him duel just like they did in some of the older games. They also did it for Tristan, Serenity, Mokuba, etc. And Mokuba is even here as well.
Because Konami has done it before, and they can do it again if they want to. After all, Mokuba was not a real duelist and had no real deck of his own in the anime/manga, and yet here he is with his own Blue-Eyes. Konami does not necessarily have to go by what cards the characters did or did not use canonically in the anime when they make the games. They can make them use whatever they want.