I don't know where you guys are getting the 1.5m projection by the end of the year.
http://ir.capcom.co.jp/english/data/pdf/fy2010_1st_quarter_a.pdf
Page 8 shows that Capcom expects 2m MH3 units shipped by March 2010, and some of those units will be going to the west in the March 2010 year. Capcom doesn't seem to have ever expected to ship 2m MH3 copies in Japan in a single year, so any speculation is just a shot in the dark. Personally, I think Capcom expect the game to ship around 1.3m-1.5m in Japan. If the game releases in the West in say, February 2010 they'd have a chance at shipping the rest of the units by the March 2010.
We already know they shipped over 1m because page eight on that document says they did, and you have to figure they'll ship at least 200k in the west, particularly if Nintendo helps Capcom promote the game. Say Capcom shipped 1.05m week one in Japan. The initial shipment has seen 80% sell through, so some stores will have sold out. That means they can ship more to replenish supply.
I can't seem Japan shipments coming in under 1.25m in the fiscal year, and western shipments should be 200k or more. So it isn't like the game missed by a huge amount. Japan is probably on the low end of their expectations, but my feeling is it will actually hold up pretty well once it gets to 5,000-10,000/week. Then it will come back a bit when the big fall Wii games lift hw over Dec-Jan. Furthermore, there isn't a Wii game out there that can't make a profit on shipments of over a million units, and the game could have something like 100,000 users paying for online content by March 2010. Nintendo probably has also given Capcom a significant royalty break on the game because they included the classic controller pro and drove the online Wii adoption significantly in Japan.