I’m not sure how much I agree with your first paragraph. Darwin’s writing can be quite dense with excessive numbers of clauses, so I may have misinterpreted. But, it seemed to me that he was not conveying that earlier versions of adaptations and organisms are inferior. If he was, I think he was referring to inferiority in terms of an organism’s successful adaptation to an environment. For instance, woodpeckers with longer beaks tend to get more food, and in this sense their adaptations are “superior,” not because there is some innate quality of superiority to having a longer beak, but because it is more successful and is more likely to be past on. If using this definition, any adaptation can be inferior or superior depending on the constraints of the surrounding ecosystem. Evolution DOES tend to improve on adaptations, not because beneficial mutations are really common, but because unsuccessful organisms die off, leaving those who are relatively more successful to reproduce. Also, I don’t believe most mutations are deleterious. My impression is that most have no effect on an organism’s survival. Most variability that occurs makes little difference to an organism’s success until a happenstance change in the environment selects certain individuals and reinforces those variations.
He does use the word “lower” to refer to organisms less successful than humans. He may be implying a sort of evolutionary direction toward “higherness” that doesn’t necessarily happen with evolution, but I can’t say he’s incorrect in conceptualizing species this way. There is degree of accuracy in calling us (or at least our minds) higher than other organisms.