Agreed.
Plus, it's not like the stats, at least the ones in this case, defensive stats, are devoid of observational data. UZR is a play by play stat. They review each chance by each fielder, note where the player is positioned before the pitch, note how hard the ball was hit, and then award/deduct points from the player's total based on how often that play is made by an average fielder. It is watching the games. It's watching them with the focus solely on what it is attempting to measure. I'll agree, there is some subjectivity there, but I have more faith that the people contributing to the metric have more focus on what they are attempting to measure than the guy chugging beers in the bleachers.
So, in the end, when this stat says Jeter had a better year than previous years, I'll trust it, because I'll eat my shoe before I believe Gom had the same focus, not to mention that he recorded his observations and conducted a tally at the end of the season.