Re: Drew Stubbs
I'm not sure that it's as much about instincts as it is simply matching up expected behavior with skill set. Stubbs is and probably always will be a poor contact hitter. Batting leadoff, he was encouraged to both see pitches for the sake of the guys behind him and to put the ball in play. This put him behind in the count and then encouraged him to swing -- a death sentence for a guy with contact problems. Batting lower in the order, he's freed up to simply find a pitch he can hit and put wood on it.
Phillips, by contrast, is a decent contact hitter. But batting cleanup, he wasn't as willing to shorten up his stroke and drive the ball where it was pitched. Cleaning up fed in to a power-hitter mentality that really didn't suit his skill set. I think batting at the top of the lineup has forced in to play more to his actual strengths as a hitter.
Games are won on run differential -- scoring more than your opponent. Runs are runs, scored or prevented they all count the same. Worry about scoring more and allowing fewer, not which positions contribute to which side of the equation or how "consistent" you are at your current level of performance.