My opinion - This kind of scares me because I feel as if they don't expect the game to sell well. I know they say that's not the reason for the drop but that's just PR crap talk. I guess the increase in sales day 1 will balance out the $39.99 price tag. I just want this game to do good so that Sony can have confidence in bringing back series such as Jak & Daxter and make a proper Ratchet and Clank game. Also, to continue Sly Cooper.
They most likely saw what happened to Starhawk (retail version), LittleBigPlanet Karting and to a lesser extent PSASBR and decided that it would be better off as a $40 title.
Since the the dev costs weren't as high as other blockbuster exclusives, they may afford a reduced retail price.
After all it worked insanely well for Sniper Ghost Warrior.