Ryou is the spitting image of his mother. We see a split second shot of Mr. Bakura from behind in the anime, and he has dark blue hair. So, that would lead me to assume (as if genetics work in this series) that he would look like his mother more than his father.
Kaiba, on the other hand, looks like his birth father. Same brown hair and lean, tall build, but maybe he has his mother’s eyes. It’s kind of hard to tell because I think that Kaiba and Mokuba both have blue eyes in the anime, just different shades. With that said, Mokuba looks like their birth mother, leading me to believe that it isn’t Mokuba that is emulated in the Virtual World game, but really their mother.