After the time skip I readied my tear ducts expecting the story would follow the characters as they got older and older until it was Rin taking care of an elderly Daikichi, but what happened instead was a whole lot of high school drama. Granted it was handled better here than in a lot of other manga (which isn't saying much), but once it moved away from the parent-child relationship it started to lose focus, and even though the characters were older it felt more shallow. As others have mentioned I disliked the way many of the secondary characters, especially Kouki's mom, were shunted off to the side.
I don't want to pass judgement on the romantic resolution because I recognize that, no matter how alien their way of thinking is to me, there are probably people out there who live in similar situations and are happy. And in fact I do think I could have appreciated the ending had the execution been better, but in addition to how it all came out of nowhere (yes, there were a few ambiguous hints here and there, but that's no replacement for proper build-up), I was dismayed by how seemingly the only major stumbling block was their distant blood connection and not the father-daughter relationship they'd cultivated over ten years. Not only does that not make a whole lot of sense, it also felt like a betrayal of the first part in which biology is secondary to the fact that he was willing to step up and be a parent to her when not even her birth mother would. The second part isn't exactly bad taken on its own terms, but as a continuation of the first it sorely disappoints.