Another great game exemplifying that a "minimalist" game doesn't have to be stingy with the game play.
I actually rather liked the fact that the one level had unused stones. Made it a bit more tricky to figure out. I wouldn't do it often, necessarily, but I liked the idea. I also liked the shallow difficulty curve, where it only gradually got harder as the player progresses.
The only suggestion I'd make is some sort of "pause"-like screen when you beat a level, so you can actually see the solution in play. Maybe have something like "Congratulations" and an arrow to take the player to the next level or something. Once you solve the puzzle it's gone in a blink of an eye. That's not a major detraction, really, but it's something I'd've liked.