When the count is 3-2 with two out and a runner on first, the runner will always go on first movement. Why does the pitcher not throw over to first to either pick off the runner or at least make him hesitate for an extra moment?
It would be a mistake for pitchers to first with 100% frequency because:
Would result in less pick offs as it would make the runner more cautious. From a game theory point of view, trying to pick off the batter less than 100% of the time is optimal as it will increase the likelihood of surprise and success (with the batter being less cautious than if the frequency was 100%)
Fear of a balk call prevents this practice once the wind up has begun: "With runners on base, after the pitcher goes into his wind-up or makes any movement associated with delivering the ball to home plate, the pitcher must not interrupt his motion or the umpire can call a balk. A balk occurs when a pitcher tries to catch a runner off base with a pick-off throw after he has started his delivery to the batter." http://www.dummies.com/how-to/content/understanding-baseballs-balk-call-and-how-to-avoid.html
There is always a small risk of making a bad throw to first or the first baseman making an error instead of a catch.
Unlike other scenarios where there is not a full count or two outs already, one more strike will end the inning. Throwing one more strike should be the primary focus of the pitcher and is far easier to achieve statistically than picking off the batter on first.
Pitchers throw over on full counts all the time. There is nothing magical about what you are saying. Yes the runner goes, but the runner hesitates until the pitcher is moving forward and then they run all out. There is hardly ever a pick-off in this situation and is usually just so the runner doesn't hit second before the pitch get so the plate or just to waste a little time.