Miyamoto was expecting more sales from Japan. It barely broke 500,000 when he made that comment, if that. I imagine it has to do with the fact TP was overly cliche (people don't except it though), had horrid audio production values (Even for Midi standards). The gameplay was rehashed, despite what other will say, and items were not used that often out of their dungeon. Maybe one or two, but most of them no. It had nice graphics, but Japan isn't as big on graphics as we are. I am not saying that these make the game bad per se, but those are potential factors to TP not doing so well in Japan.
SMG is selling very normal for a Mario platformer. People are assuming that Japan is being lazy again with its poor sales compared to the US, but Mario platformers aren't that big over there. It already broke 1,000,000 worldwide a week after release, so it is doing fine. I lot of people can't comprehend that it isn't unusual for a Mario spin-off DS game to outsell a canon Mario Wii game in Japan. Back when Nsider was open, I was talking with a person who lived in Japan (Razzalyn for those who there before it closed), and she mentioned that spin-off games were more popular than canon games.