Finished Refrain 2 days ago. I have no guarantees this is going to be a coherent post of any sort... but here goes.
Some shenanigans were suspected as early as Kurugaya's route. There was some hint there that was dropped which indicated some kind of time loop device was at work and that something about this world was not quite right. Knowing the secret of the world, I still am not sure what's going on in her route.
I think Refrain hit me really hard, because we had spent the last tens of hours of reading getting to know these characters and knowing that they were going to be taken away from me was cruel and heartbreaking. The scene at the end with Rin and Komari were especially good at this. We end the story with Rin and Riki. I don't know if I wanted it to go any other way though. The idea that these two are the only survivors of their circle of friends, carrying the memories of their friends and the strength they gained from redoing the world over and over, is a powerful one.
And then Little Busters! in the fine tradition of the late Billy Mays, goes "But wait, there's more!"
I'm very conflicted on the final happy ending, because I feel like it was too miraculous to undo everything literally seconds after the ending credits played. If I had to say there was a set of themes for Little Busters, one would be that we can overcome challenges together that we could not overcome alone, and we can have fun doing it. There was price to be paid or challenge to overcome together. The events are described as miraculous, as if a divine being (like Dorj) willed it into existence. The other would be that circles of friends cannot last forever and we have to say goodbye to our friends one day, maybe temporarily as in Kud and Rin's routes or maybe we may never see them again. Of these, the second one hit me harder, and I wish the final ending committed to that theme with more confidence.