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If the AI takes the best hitter at each position and puts them in the lineup, it won't matter where they are in the batting order in terms of generating runs for the team. You could take the 1927 Yankees and bat Ruth and Gehrig 1-2 in the order and they'll score just as many runs as if you hit them 3-4. Or you could put your worst hitter at leadoff and still end up with the same offensive output.
Having said that, OOTP does a very good job at formulating the lineups IMO. Basically the 2 best OPS guys will end up 3-4 in the lineup, the next 2 best available OBP guys will hit 1-2, and the remaining 5-8 hitters will be in descending order of projected OPS. That's basically a good way to create a realistic lineup and seems to be what OOTP tries to do.
pstrickert - "Who's to say, though, that IRL the bench player would have produced the same numbers if his manager had made him the starter for the whole season?" That's why in the neutralized DB we make sure that all players have at least 251 AB in each of their season's batting lines. In cases where they didn't have that many IRL we pro-rate the missing AB with the average from their career or their surrounding seasons. Now, when you use 3-yr recalc, the AI is always going to be looking at a minimum of 502+ AB (rookies) and 753+ AB for anyone else. That's a good sample size to make decisions with. Yes, hindsight is 20/20, but the AI should have the same advantage as the human manager.
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