This will hurt Murray's chances of finishing 2012 #1 or #2.
Murray I believe lost all 250 from not replaying Bangkok, and then for only making the SF here in Tokyo he loses some more big points. He likely won't win Shanghai again, in fact I don't think he'll make it past the SF, so that's another 640 point loss.
Murray is bound to finish 2012 #3. Rafa/Ferrer for #4 and #5 (probably Rafa stays 4 and Ferrer 5 or lower), and the battle for #1 and #2 is between Rogie and Djokovic.
Murray was never getting to #1 this year. With our without this title.
The last guy who defended this title was Pete Sampras in 1994. It's just not meant to be I suppose.
Andy was outplayed for most of the match and then didn't take his chances in the 3rd. Milos deserved to win here.