I genuinely love the fact that the first thing he did was actually apologise. He understood how he messed up, and that the first thing to do is to own up to it.
The manga ends well with the girl graduating, but then the author added an epilogue set a couple of years in the future with the same ending as Usagi Drop but without all the drama. In my mind, the epilogue isn't canon; I don't know why authors do this.