As it turns out, we've been tracking player-vs-player and player-vs-team results since 2007. So here's some info in case you didn't know how to access this feature:
1. On the charts tab in the Scouting Report, click on the gray box that shows what is currently being displayed (batting average, 2 outs, etc.) and you will get a dialog box that lets you choose vs-player or vs-team:
2. Stats by each team's lineup versus the other team's pitchers are shown at game start (when selecting a starter or adjusting the lineup). For example, this screen shot shows a player comparing the career performance of two pitchers against the Yankees:
3. During game play, head-to-head stats are shown under the batter's scouting report.