Since people are still talking about this, I might as well chime in.
I had read Usagi Drop many years ago, then dropped it a little after the time-skip. What I'm going to say is this: Even if we can't agree on whether the final pairing itself was bad or not... (personally it leaves me coldly indifferent)
...can we agree that the time-skip itself was written very, very poorly? I mean, the mere fact that it leaves you wondering "Wait, did I miss 10 chapters or something?" is bad enough, but this could be forgivable. But what really grated on my nerves was the "Oh, you know those things we established in the previous chapters? Nope, they aren't true." angle it took. It's so logically disjoint from the first half that it reads like the first steps of a particularly low-quality fanfic; in short, it's plain shoddy writing.
So, to the fine and honourable people who liked the ending, I ask this: Can we agree that the transition from A to B was done in a shoddy manner? Or do you find me mistaken in my assessment?