I don't know how this is questionable in any way. They were never really in a parent-child relationship from the beginning, as even the most basic things got skipped/passed, like the story where Daikichi offered Rin to adopt her to make her carry his surname with her refusing to do so.
If he ever thought of her as his daughter, it would've been the first step to take before even taking her in in the first place. He just wanted to lower her social pressure since her circumstances were not normal at all.
This is, generally speaking, on a totally different level of inter-human relationship, more like a friend wanting to help his friend to overcome a certain circumstance instead of taking the initiative of parental duty [ which usually is the one-sided concern of the parent for its child, hence taking the best measures to ensure the childs well-being]. That way it continued throughout the manga, reminding me a little of "Kodomo no Jikan" for that aspect alone.
It's also a good material to compare to since it features both the age-gapped inter-human relationship [Aoki x Rin] and the parent[guardian]-child relationship to compare and uses the theme as a plot element [Aoki believes at a certain point that his relationship with Rin is like a father-daughter relationship].
From what I've understood by reading and comparing both stories, it's basically the wrong conception of the aspect of "family" that makes readers forward their disapprovement in terms of such developement/relationships; It's mainly based on the wrong assumption that family is based only on age-differences, and that the older party is basically always the "elder"[parent/grandparent/uncle-aunt]. This totally ignores the fact that, regarding the family composition and the possible ages of the members, there can also be settings where the age difference between siblings would be more like "father&daughter" or "mother&son".
With this in mind, we can assume that there is the basic concept of family and friendship for this setting. However, if there are no blood ties between the characters, it's not unlikely for people to become attracted to each other. The male brain is [normally at least] concipated to be attracted to the sight of the grown-up female body, the same goes for the female brain in case of the male body. Living together under the same roof and spending long years together drastically increases the chances to become attracted to that person, because you have higher interaction-levels with that certain someone.
This can reach from intimate friendship [also called brocon/siscon or equivalents for father/mother/uncle/aunt] to full-fledged sexual attraction.
So, following this, if we set aside the age difference, the story is not that different from all that foster child x child relationships between step siblings; those stories often feature special bonds between the cast and a deep family-care for the respective other, usually with one party being sacrificial to a certain extend [the guy working early to provide for the family or the girl doing all the chores on her own e.g.]. This is exactly what happens here, the only difference is that we get a deeper insight on the life of the party that "sacrifices"[usually that character is not the main character in stories who focus on romance and family settings] instead of the life of the person who gets "pampered".
This was used to an extend to create a deeper level of storytelling in Kodomo no Jikan by unravelling the social circumstances of Rin, creating a fundamental rift of that story that created so many social controversities in Japan.
This is also why we basically might consider this flow of events in Usagi Drop "strange" or not fullfilling, because we were "fed" something that's surprisingly different from what we thought, though the ending being a little obvious given by the scattered hints throughout the story. It was just way less straight-forward than Kodomo no Jikan, and thus, less provoking.
Nowadays where mockery of logic is nearly omnipresent in manga, I think it's nice to see one story where science and logic actually result in an understanding of characters and story to an extend where they feel human&real in contrast to being just a few lines on a blank paper filled with thoughts of a non-realistic person [i.e. the author; non-realistic because he isn't part of the concept/story, thus a being of "god"/laplaces demon status for the reader as he can't comprehend the thoughts on an unknown entity]. It's well done and fair enough for the mature reader I think, if you try to break the 4th wall and try to conceive everything more sophistically.