I'll post on this thread again just to say that I think both you guys are right to some extent.
Yes, the AI does a pretty good job of creating lineups. In fact, I think it does remarkably well considering that it's an AI.
Yes, the AI does some things with lineups, from time to time, that would never happen in real life.
Yes, when the AI does these eccentric things, they sometimes make some sense, and probably should have been considered by real life managers (LaRussa's reputation, notwithstanding

). Otherwise they are just anomalies.
Yes, it sure seems like the game engine could factor in, and give some weight to, data on how often a player started in each slot of a lineup (at the game player's option). I think that would be a great compromise. But maybe that data isn't in the Lahman DB, so it couldn't be done. Don't know, but that might end the debate right there.