I guess the biggest thing is, if Philip II was so smart, why was it Alexander who became Lord of Asia and not him? Oh right, because as even Machiavelli (otherwise a fan of Philip II) notes in the Discourses, he got killed because he didn't avenge Pausanias after he was raped despite multiple complaints. So much for the pragmatic genius. And it's not like Philip invented the idea of the phalanx, though yeah he was a pretty incredible military organizer.
Did Philip even have the ambition or desire needed to conquer Persia? Would he have had the tolerance needed to actually rule these areas that Alexander demonstrated (i.e. marrying Roxane despite it upsetting "old guard" generals, keeping in place a lot of the local government structures/making deals with people like Porus) or would he have insisted on violent rule that would have created conditions ripe for rebellion?
Alexander had to fight in insane conditions against armies with elephants in India. And he won. Yes he inherited a lot, but I think he's more versatile than implied here.