After you beat Route A, you're explicitly told to keep playing to find out more about the story. The beginning of Route B lays a strong foundation that you'll see more about 9S, his role, and filling in the holes of his story from A. Then, when B still ends at the same place, you get the C/D preview which is a new Route of the campaign. The logical flow is there if you have intrigue in the story, but I can see why people wouldn't care (which is a shame if you ask me). But I can't agree with calling it "misleading."
Also, while the game has 5 story endings, we're effectively talking about 3 playthroughs. After C or D, you get scene select, which can put you right at the C/D split, and once you've done both C and D, you get the option to finish with E. The difference between 3 and 5 here is substantial.