I think that's where you're wrong. Of course you look to make improvements. But you don't do it by moving your BEST players to a new position. You get rid of Fosse and Green because they can't hit their weight. And everyone says, if it doesn't work, "Well, ****, they couldn't hit their weight". You move your franchise player to LF, lose and everyone says "What the **** was that about?" You have emotion, ego, continuity, chemistry, pride and any number of other things that aren't in play when looking at a bunch of stats. Upsetting the apple cart, if you will. IMO, the baseball world would have said "Damn, if they'll do that to Jeter, how would they treat me?" And no big name FA would ever come to NY.
As for fielding vs. bat, of course that's what it's about. What you lost in the field, you more than made up with the bat. We're not talking about Greg Luzinski playing SS. Jeter was slightly below average. He wasn't a butcher with a stone glove. He made the plays that he could get to. Personally, I always felt he was out of position way too much. Maybe he was cheating to help his lack of range or maybe they had him cheating in an attempt to cover his lack of range. Either way, he was kicking routine balls.
At the end of the day, people who know more baseball than you and I said "We can work with that." And they won. A lot. The results are what they are.